Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 106 of 182
Found at i:34443537 original size:89 final size:89
Alignment explanation
Indices: 34443393--34443614 Score: 286
Period size: 89 Copynumber: 2.5 Consensus size: 89
34443383 AATTTTGGAA
* * *
34443393 AAAGTTTGGGGGTCAAAAATGTAATTTTTAAAAAGTTTAGGGATTAAAATGTAATTTTTAGAAAG
1 AAAGTTTAGGGGTC-AAAATGTAATTTTTAAAAAGTTTAGGGATTAAAATATAATTTTTAAAAAG
*
34443458 TTTT-GGGCCAAAATGTAATGTTTAG
65 TTTTGGGGCCAAAATATAAT-TTTAG
*
34443483 AAAGTTTAAGGGTCAAAATGTAATTTTTAAAAAGTTTTAGGG-TTAAAATATAATTTTTAAAAAG
1 AAAGTTTAGGGGTCAAAATGTAATTTTTAAAAAG-TTTAGGGATTAAAATATAATTTTTAAAAAG
* *
34443547 TTTTGGGGTCAAAATATAATTTTGG
65 TTTTGGGGCCAAAATATAATTTTAG
* * * * *
34443572 AAATGTTCAGGGGTCAAAATATAATTTCTAGATAGTTTAGGGA
1 AAA-GTTTAGGGGTCAAAATGTAATTTTTAAAAAGTTTAGGGA
34443615 CCTATAAGCA
Statistics
Matches: 115, Mismatches: 13, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
89 58 0.50
90 57 0.50
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.37
Consensus pattern (89 bp):
AAAGTTTAGGGGTCAAAATGTAATTTTTAAAAAGTTTAGGGATTAAAATATAATTTTTAAAAAGT
TTTGGGGCCAAAATATAATTTTAG
Found at i:34443560 original size:60 final size:59
Alignment explanation
Indices: 34443376--34443569 Score: 217
Period size: 59 Copynumber: 3.2 Consensus size: 59
34443366 GTTCGAAGGT
* * * * *
34443376 AAAATCTAATTTTGGAAAAAGTTTGGGGGTCAAAAATGTAATTTTTAAAAAGTTTAGGGATT
1 AAAATGTAATTTT-TAAAAAGTTT-TGGGT-AAAAATGTAATTTTTAAAAAGTTTAGGGGTC
* ** * * *
34443438 AAAATGTAATTTTTAGAAAGTTTTGGGCCAAAATGTAATGTTTAGAAAGTTTAAGGGTC
1 AAAATGTAATTTTTAAAAAGTTTTGGGTAAAAATGTAATTTTTAAAAAGTTTAGGGGTC
* * *
34443497 AAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATATAATTTTTAAAAAGTTTTGGGGTC
1 AAAATGTAATTTTTAAAAAGTTTT-GGGTAAAAATGTAATTTTTAAAAAGTTTAGGGGTC
*
34443557 AAAATATAATTTT
1 AAAATGTAATTTT
34443570 GGAAATGTTC
Statistics
Matches: 111, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 48 0.43
60 43 0.39
61 8 0.07
62 12 0.11
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (59 bp):
AAAATGTAATTTTTAAAAAGTTTTGGGTAAAAATGTAATTTTTAAAAAGTTTAGGGGTC
Found at i:34443790 original size:21 final size:22
Alignment explanation
Indices: 34443755--34443797 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
34443745 TTTTTTTTAA
34443755 TATTATTATTTATTAAAACATT
1 TATTATTATTTATTAAAACATT
34443777 TATTATTA-TTATTAAAACATT
1 TATTATTATTTATTAAAACATT
34443798 AATACTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATTATTTATTAAAACATT
Found at i:34444597 original size:6 final size:6
Alignment explanation
Indices: 34444581--34444661 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
34444571 AATTTATATT
*
34444581 AATTCTA AATTTA AA-TTA AATTTA AATTT- AA--TA AATCTA AATTTA
1 AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
34444626 AA-ATA AATTTA ACTTTA ACA--TA AATTTA ATTTTA AA
1 AATTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA AA
34444662 ATGAATTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
3 1 0.02
4 3 0.05
5 14 0.24
6 37 0.63
7 4 0.07
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:34444602 original size:11 final size:11
Alignment explanation
Indices: 34444586--34444637 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
34444576 ATATTAATTC
34444586 TAAATTTAAAT
1 TAAATTTAAAT
34444597 TAAATTTAAAT
1 TAAATTTAAAT
*
34444608 TTAA--TAAAT
1 TAAATTTAAAT
*
34444617 CTAAATTTAAAA
1 -TAAATTTAAAT
34444629 TAAATTTAA
1 TAAATTTAA
34444638 CTTTAACATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 5 0.14
10 3 0.09
11 23 0.66
12 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:34444630 original size:17 final size:17
Alignment explanation
Indices: 34444550--34444669 Score: 111
Period size: 17 Copynumber: 7.1 Consensus size: 17
34444540 GGACACTCTA
* *
34444550 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
* *
34444567 TTAAAATTT-ATATTAAT
1 TT-AAATTTAAAATAAAT
*
34444584 TCTAAATTTAAATTAAAT
1 T-TAAATTTAAAATAAAT
34444602 TTAAATTT--AATAAAT
1 TTAAATTTAAAATAAAT
*
34444617 CTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
34444634 TTAACTTTAACATAAAT
1 TTAAATTTAAAATAAAT
* *
34444651 TTAATTTTAAAATGAAT
1 TTAAATTTAAAATAAAT
34444668 TT
1 TT
34444670 TAAAATGATT
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
15 13 0.16
17 57 0.69
18 13 0.16
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:34444668 original size:12 final size:12
Alignment explanation
Indices: 34444653--34444677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34444643 ACATAAATTT
34444653 AATTTTAAAATG
1 AATTTTAAAATG
34444665 AATTTTAAAATG
1 AATTTTAAAATG
34444677 A
1 A
34444678 TTTGGCTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:34445094 original size:92 final size:92
Alignment explanation
Indices: 34444937--34445694 Score: 1419
Period size: 92 Copynumber: 8.2 Consensus size: 92
34444927 GAGGTTTTAT
*
34444937 CTTCAGAGAGATAAATG-TTCATTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACAT
1 CTTCAGAGAGATAAA-GATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACAT
34445001 TTGAAAATTCATCTTGCTCTTACTATAA
65 TTGAAAATTCATCTTGCTCTTACTATAA
*
34445029 CTTCAGAGAGATAAAGATTCGTTATCCAGCTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
34445094 TGAAAATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
*
34445121 CTTCAGAGAGATAAAGATTCGTTATCGAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
34445186 TGAAAATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
*
34445213 CTTCAGAGAGATAAAGATTCATTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
34445278 TGAAAATTCATCTTGCTCTTAGTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
34445305 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
34445370 TGAAAATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
*
34445397 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGGCATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
34445462 TGAAGATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
*
34445489 CTTCAGAGAGATAAAGATTCGTTATCGAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
*
34445554 TGAAAATTCATCTTGCTGTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
34445581 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
1 CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
34445646 TGAAAATTCATCTTGCTCTTACTATAA
66 TGAAAATTCATCTTGCTCTTACTATAA
34445673 CTTCAGAGAGATAAAGATTCGT
1 CTTCAGAGAGATAAAGATTCGT
34445695 CGTCGTGGAT
Statistics
Matches: 648, Mismatches: 17, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
91 1 0.00
92 647 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (92 bp):
CTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTTCAAGAGGATAAGAATTGACATT
TGAAAATTCATCTTGCTCTTACTATAA
Found at i:34456819 original size:96 final size:97
Alignment explanation
Indices: 34456638--34456816 Score: 220
Period size: 96 Copynumber: 1.9 Consensus size: 97
34456628 AATTTTAGGA
*** * * * *
34456638 AAGGGATATTCGATTATCTTGATTTAAAGAAGGGTTGCACCTAGTGAGTTAATGCGCAAATTTTC
1 AAGGGATATTCGATTATCTTGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAAAATTTC
*
34456703 AAAGATCGAAGATAAGAAATATCGCCTTGATT
66 AAAGATCGAAGATAAAAAATATCGCCTTGATT
* * *
34456735 AAGGG-TATTCGATTATTTTGGTTTGAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAAAATTTC
1 AAGGGATATTCGATTATCTTGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAAAATTTC
*
34456799 GAAA-CTCGAA-ATAAAAAA
66 -AAAGATCGAAGATAAAAAA
34456817 ATAACCTCGA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
95 7 0.10
96 54 0.78
97 8 0.12
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.30
Consensus pattern (97 bp):
AAGGGATATTCGATTATCTTGATTTAAAGAAAAATTGCACCTAGTAAGTTAAGGAGCAAAATTTC
AAAGATCGAAGATAAAAAATATCGCCTTGATT
Found at i:34457070 original size:29 final size:29
Alignment explanation
Indices: 34457037--34457114 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 29
34457027 TTTGGATACC
*
34457037 CGGGTGTAAAATGGTAATTTAGTTAGAA-TT
1 CGGGTGCAAAATGGTAATTT--TTAGAAGTT
*
34457067 -GGGT-CAAAATGG-GATTTTTAGAAGTT
1 CGGGTGCAAAATGGTAATTTTTAGAAGTT
*
34457093 CGGGGGCAAAATGGTAATTTTT
1 CGGGTGCAAAATGGTAATTTTT
34457115 GGTGAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
25 6 0.15
26 2 0.05
27 7 0.17
28 15 0.38
29 10 0.25
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (29 bp):
CGGGTGCAAAATGGTAATTTTTAGAAGTT
Found at i:34457226 original size:30 final size:30
Alignment explanation
Indices: 34457067--34457312 Score: 130
Period size: 30 Copynumber: 8.1 Consensus size: 30
34457057 AGTTAGAATT
** * *
34457067 GGGTCAAAATGGGATTTTTAG-AAG-TTCG
1 GGGTCAAAATGTAATTTTTGGAAAGTTTAG
*
34457095 GGGGCAAAATGGTAATTTTTGGTGAAA--TTAG
1 GGGTCAAAAT-GTAATTTTT-G-GAAAGTTTAG
* * ** *
34457126 GGTTAAAAATGGGA-TTTTGGAAAGTTCAG
1 GGGTCAAAATGTAATTTTTGGAAAGTTTAG
* * * *
34457155 AGGT-AAAATCTAA-TTTTGGAAATTTTTGG
1 GGGTCAAAATGTAATTTTTGGAAA-GTTTAG
*
34457184 GGGTCAAAAATGTAATTTTTAGAAAGTTTAG
1 GGGTC-AAAATGTAATTTTTGGAAAGTTTAG
** *
34457215 GGGTCAAAATGTAATTTTTATTTTCAAAAAGTTTTG
1 GGGTCAAAATGTAA----T-TTTT-GGAAAGTTTAG
*
34457251 GGGTCAAAATATAA-TTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTTGG-AAAGTTTAG
* * *
34457281 AGGTCAAAATATAATTTTTGGATAGTTTAG
1 GGGTCAAAATGTAATTTTTGGAAAGTTTAG
34457311 GG
1 GG
34457313 ACCTATAGGC
Statistics
Matches: 167, Mismatches: 33, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
27 4 0.02
28 25 0.15
29 22 0.13
30 45 0.27
31 34 0.20
32 10 0.06
34 1 0.01
35 4 0.02
36 22 0.13
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTTAG
Found at i:34459256 original size:6 final size:6
Alignment explanation
Indices: 34459209--34459337 Score: 75
Period size: 6 Copynumber: 22.8 Consensus size: 6
34459199 GGACACTCTA
*
34459209 TTAAAT TTATAA- -TAAAT TTAAAAT TTACA- TT-AAT TCTAAAT TTAAA-
1 TTAAAT TTA-AAT TTAAAT TT-AAAT TTAAAT TTAAAT T-TAAAT TTAAAT
* * *
34459255 TTAAAT TTAAAT TT-AA- -TAAAT CTAAAT TTAAA- ATAAAT TTAACT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
34459299 TTAACA- -TAAAT TTAATT TTAAA- ATAAAT TTAATT TTAAA
1 TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
34459338 ATGAATTTTA
Statistics
Matches: 94, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
3 1 0.01
4 6 0.06
5 23 0.24
6 52 0.55
7 12 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:34459261 original size:11 final size:11
Alignment explanation
Indices: 34459208--34459330 Score: 74
Period size: 11 Copynumber: 11.0 Consensus size: 11
34459198 TGGACACTCT
34459208 ATTAAATTTATA
1 ATTAAATTTA-A
34459220 A-TAAATTTAAA
1 ATTAAATTT-AA
*
34459231 ATTTACA-TTAA
1 A-TTAAATTTAA
*
34459242 TTCTAAATTTAA
1 AT-TAAATTTAA
34459254 ATTAAATTTAA
1 ATTAAATTTAA
*
34459265 ATTTAA--TAA
1 ATTAAATTTAA
34459274 ATCTAAATTTAA
1 AT-TAAATTTAA
*
34459286 AATAAATTTAA
1 ATTAAATTTAA
* * **
34459297 CTTTAACATAA
1 ATTAAATTTAA
*
34459308 ATTTAATTTTAA
1 A-TTAAATTTAA
*
34459320 AATAAATTTAA
1 ATTAAATTTAA
34459331 TTTTAAAATG
Statistics
Matches: 83, Mismatches: 19, Indels: 19
0.69 0.16 0.16
Matches are distributed among these distances:
9 5 0.06
10 4 0.05
11 51 0.61
12 20 0.24
13 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:34459338 original size:17 final size:17
Alignment explanation
Indices: 34459209--34459345 Score: 145
Period size: 17 Copynumber: 8.1 Consensus size: 17
34459199 GGACACTCTA
*
34459209 TTAAATTTATAATAAAT
1 TTAAATTTAAAATAAAT
* *
34459226 TTAAAATTT-ACATTAAT
1 TT-AAATTTAAAATAAAT
*
34459243 TCTAAATTTAAATTAAAT
1 T-TAAATTTAAAATAAAT
34459261 TTAAATTT--AATAAAT
1 TTAAATTTAAAATAAAT
*
34459276 CTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
34459293 TTAACTTTAACATAAAT
1 TTAAATTTAAAATAAAT
*
34459310 TTAATTTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
34459327 TTAATTTTAAAATGAAT
1 TTAAATTTAAAATAAAT
34459344 TT
1 TT
34459346 TAAAATGATT
Statistics
Matches: 101, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
15 13 0.13
17 75 0.74
18 13 0.13
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:34459344 original size:12 final size:12
Alignment explanation
Indices: 34459329--34459353 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34459319 AAATAAATTT
34459329 AATTTTAAAATG
1 AATTTTAAAATG
34459341 AATTTTAAAATG
1 AATTTTAAAATG
34459353 A
1 A
34459354 TTTGGCTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:34462400 original size:27 final size:27
Alignment explanation
Indices: 34462350--34462402 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
34462340 TGTAAATATG
* *
34462350 TTTTTTATTTTTATTTTTTATTTGTAA
1 TTTTATATTTTTATTTATTATTTGTAA
34462377 TTTTATATTTTTATATTATT-TTTGTA
1 TTTTATATTTTTAT-TTATTATTTGTA
34462403 TAATTAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (27 bp):
TTTTATATTTTTATTTATTATTTGTAA
Found at i:34473347 original size:2 final size:2
Alignment explanation
Indices: 34473340--34473371 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34473330 TGGTTAAAAT
34473340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34473372 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34477150 original size:68 final size:69
Alignment explanation
Indices: 34477018--34477157 Score: 192
Period size: 68 Copynumber: 2.0 Consensus size: 69
34477008 ATTTTCTTAC
** *
34477018 CAAACTACTAAATTTATTAATTAGCAATATTCCAAGCAATATATTAAAACAAGTAATTTGTGCTA
1 CAAACTACTAAATCAATTAATTAGCAATATTCCAAGCAATATATTAAAACAAGTAATTTATGCTA
34477083 TATT
66 TATT
* * * * * *
34477087 CAAACTACTAAATCAATTAATTGGC-ATATTCCAAGCACTATGTTCAAAGAAGTACTTTATGCTA
1 CAAACTACTAAATCAATTAATTAGCAATATTCCAAGCAATATATTAAAACAAGTAATTTATGCTA
34477151 TATT
66 TATT
34477155 CAA
1 CAA
34477158 CCTCCAGACT
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
68 40 0.65
69 22 0.35
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (69 bp):
CAAACTACTAAATCAATTAATTAGCAATATTCCAAGCAATATATTAAAACAAGTAATTTATGCTA
TATT
Found at i:34479077 original size:15 final size:13
Alignment explanation
Indices: 34479064--34479100 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
34479054 TTATTTTATT
34479064 TTTAATTTTTTTA
1 TTTAATTTTTTTA
34479077 TTTAATTTTTATTA
1 TTTAATTTTT-TTA
34479091 CTTTAATTTT
1 -TTTAATTTT
34479101 AATTAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.45
14 3 0.14
15 9 0.41
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTAATTTTTTTA
Found at i:34479080 original size:13 final size:15
Alignment explanation
Indices: 34479064--34479105 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
34479054 TTATTTTATT
34479064 TTTAATTTTT-TTA-
1 TTTAATTTTTATTAC
34479077 TTTAATTTTTATTAC
1 TTTAATTTTTATTAC
*
34479092 TTTAATTTTAATTA
1 TTTAATTTTTATTA
34479106 GGTTTATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 10 0.38
14 3 0.12
15 13 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTAATTTTTATTAC
Found at i:34479095 original size:19 final size:20
Alignment explanation
Indices: 34479053--34479095 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
34479043 TTGGCACCTT
* **
34479053 TTTATTTTATTTTTAATTTT
1 TTTATTTAATTTTTAATTAC
34479073 TTTATTTAATTTTT-ATTAC
1 TTTATTTAATTTTTAATTAC
34479092 TTTA
1 TTTA
34479096 ATTTTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTTAATTTTTAATTAC
Found at i:34479105 original size:15 final size:13
Alignment explanation
Indices: 34479056--34479101 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
34479046 GCACCTTTTT
34479056 ATTTTATT-TTTA
1 ATTTTATTATTTA
*
34479068 ATTTTTTTATTTA
1 ATTTTATTATTTA
34479081 ATTTTTATTACTTTA
1 A-TTTTATTA-TTTA
34479096 ATTTTA
1 ATTTTA
34479102 ATTAGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 7 0.24
13 5 0.17
14 12 0.41
15 5 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTATTATTTA
Found at i:34485807 original size:17 final size:15
Alignment explanation
Indices: 34485787--34485834 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
34485777 TAATTTAGTC
34485787 AAAAGAAATAACAACTT
1 AAAAGAAATAACAA--T
* *
34485804 AAAAAAAATAATAAT
1 AAAAGAAATAACAAT
34485819 AATAAGAAATAACAAT
1 AA-AAGAAATAACAAT
34485835 TTTTGACTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.12
16 11 0.42
17 12 0.46
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAAGAAATAACAAT
Found at i:34493372 original size:36 final size:36
Alignment explanation
Indices: 34493302--34493449 Score: 190
Period size: 36 Copynumber: 4.1 Consensus size: 36
34493292 CGTATCTCAA
* * * *
34493302 ACGATCTCTTCAAGTTTCCAAAT-AATTCATCTCTT
1 ACGAGCTCTTCAAGTTTCCCAGTAAATTCAGCTCTT
34493337 ACGAGCTCTTCAAGTTTCCCAGTAAATTCAGCTCTT
1 ACGAGCTCTTCAAGTTTCCCAGTAAATTCAGCTCTT
* * *
34493373 ATGAGCTCTTCAAGTTTCCCAGTAAATCCAACTCTT
1 ACGAGCTCTTCAAGTTTCCCAGTAAATTCAGCTCTT
* * * *
34493409 ACGAGCTCTTCAAGTATCCCAGTAATTTTAGCTCAT
1 ACGAGCTCTTCAAGTTTCCCAGTAAATTCAGCTCTT
34493445 ACGAG
1 ACGAG
34493450 ACCAATCAGT
Statistics
Matches: 98, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 20 0.20
36 78 0.80
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (36 bp):
ACGAGCTCTTCAAGTTTCCCAGTAAATTCAGCTCTT
Found at i:34493473 original size:26 final size:26
Alignment explanation
Indices: 34493439--34493494 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
34493429 AGTAATTTTA
34493439 GCTCATACGAGACCA-ATCAGTAAATC
1 GCTCATACGAG-CCAGATCAGTAAATC
* * *
34493465 GCTCTTACGAGCCAGTTCAGTATATC
1 GCTCATACGAGCCAGATCAGTAAATC
34493491 GCTC
1 GCTC
34493495 CTAATACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.25
Consensus pattern (26 bp):
GCTCATACGAGCCAGATCAGTAAATC
Found at i:34499159 original size:19 final size:19
Alignment explanation
Indices: 34499135--34499210 Score: 109
Period size: 19 Copynumber: 4.0 Consensus size: 19
34499125 CAGTCAGTAA
*
34499135 ATCGCTCTTACGAGCCAGT
1 ATCGCTCTTACAAGCCAGT
*
34499154 ATCGCTCTCACAAGCCAGT
1 ATCGCTCTTACAAGCCAGT
*
34499173 AAT-GCTCTTACGAGCCAGT
1 -ATCGCTCTTACAAGCCAGT
34499192 ATCGCTCTTACAAGCCAGT
1 ATCGCTCTTACAAGCCAGT
34499211 TGAGTCTATC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
18 2 0.04
19 46 0.92
20 2 0.04
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (19 bp):
ATCGCTCTTACAAGCCAGT
Found at i:34499182 original size:38 final size:40
Alignment explanation
Indices: 34499129--34499210 Score: 141
Period size: 38 Copynumber: 2.1 Consensus size: 40
34499119 CTAGCTCAGT
34499129 CAGTAAATCGCTCTTACGAGCCAGTATCGCTCTCACAAGC
1 CAGTAAATCGCTCTTACGAGCCAGTATCGCTCTCACAAGC
*
34499169 CAGT-AAT-GCTCTTACGAGCCAGTATCGCTCTTACAAGC
1 CAGTAAATCGCTCTTACGAGCCAGTATCGCTCTCACAAGC
34499207 CAGT
1 CAGT
34499211 TGAGTCTATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 34 0.83
39 3 0.07
40 4 0.10
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (40 bp):
CAGTAAATCGCTCTTACGAGCCAGTATCGCTCTCACAAGC
Found at i:34504153 original size:2 final size:2
Alignment explanation
Indices: 34504140--34504195 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
34504130 ATTAATTTTA
*
34504140 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34504182 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
34504196 GTATGTATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34507661 original size:4 final size:4
Alignment explanation
Indices: 34507652--34507710 Score: 91
Period size: 4 Copynumber: 14.5 Consensus size: 4
34507642 TTTTACGATG
* *
34507652 TAAA TAAA TAAA TAAA TAAA TAAT TAAA TAAC TAAA TAAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA TAAA TAAA
34507701 TAAA TAAA TA
1 TAAA TAAA TA
34507711 TATATAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
4 46 0.92
5 4 0.08
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:34508042 original size:19 final size:19
Alignment explanation
Indices: 34508015--34508055 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
34508005 AATTTTTATA
*
34508015 AAATAAAATAATATTAAAT
1 AAATAAAATAAAATTAAAT
* *
34508034 AAATTAAATAAAATTAATT
1 AAATAAAATAAAATTAAAT
34508053 AAA
1 AAA
34508056 AATATTTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAAAATAAAATTAAAT
Found at i:34508056 original size:10 final size:10
Alignment explanation
Indices: 34508012--34508056 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
34508002 AGAAATTTTT
*
34508012 ATAAAATAAA
1 ATAAAATTAA
*
34508022 ATAATATTAA
1 ATAAAATTAA
34508032 AT-AAATTAA
1 ATAAAATTAA
34508041 ATAAAATTAA
1 ATAAAATTAA
*
34508051 TTAAAA
1 ATAAAA
34508057 ATATTTTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAATTAA
Found at i:34513183 original size:3 final size:3
Alignment explanation
Indices: 34513175--34513223 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
34513165 TAAATGCACT
34513175 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34513223 T
1 T
34513224 TTTAGTCATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34514118 original size:36 final size:35
Alignment explanation
Indices: 34514047--34514141 Score: 99
Period size: 36 Copynumber: 2.7 Consensus size: 35
34514037 ATATTTTTCC
* **
34514047 ATAAAAAT-AATTAAAAATTATAAAACTATTCAAT
1 ATAAAAATCTATTAAAAATTATAAAACTATAAAAT
*
34514081 ATTAAAAT-TA-TAAAAATTGATATAAACTTATAAAAT
1 ATAAAAATCTATTAAAAATT-ATA-AAAC-TATAAAAT
34514117 ATAAAAATCTATTAAAAATT-TAAAA
1 ATAAAAATCTATTAAAAATTATAAAA
34514142 AATTAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
33 8 0.16
34 11 0.22
35 7 0.14
36 15 0.29
37 2 0.04
38 8 0.16
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (35 bp):
ATAAAAATCTATTAAAAATTATAAAACTATAAAAT
Found at i:34514630 original size:19 final size:19
Alignment explanation
Indices: 34514606--34514671 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
34514596 TCACTTCAAG
34514606 TTTTTATGATTTTTTAT-AA
1 TTTTTAT-ATTTTTTATAAA
* * *
34514625 TTTTTATACGTTTATATCAA
1 TTTTTATA-TTTTTTATAAA
*
34514645 TTTTAATATTTTTTATAAA
1 TTTTTATATTTTTTATAAA
34514664 TTTTTATA
1 TTTTTATA
34514672 GAATTTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.03
19 28 0.74
20 9 0.24
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTTATATTTTTTATAAA
Found at i:34514678 original size:21 final size:21
Alignment explanation
Indices: 34514606--34514731 Score: 65
Period size: 19 Copynumber: 6.3 Consensus size: 21
34514596 TCACTTCAAG
*
34514606 TTTTTAT-GATTTTTTAT-AA
1 TTTTTATAGAATTTTTATAAA
* *
34514625 TTTTTATACG--TTTATATCAA
1 TTTTTATA-GAATTTTTATAAA
* *
34514645 -TTTTA-ATATTTTTTATAAA
1 TTTTTATAGAATTTTTATAAA
* *
34514664 TTTTTATAGAATTTTAATACA
1 TTTTTATAGAATTTTTATAAA
*
34514685 TTTTTATA-AAATTTTA-AATA
1 TTTTTATAGAATTTTTATAA-A
* *
34514705 TGTTTTAT-TAATTTAT-TAAA
1 T-TTTTATAGAATTTTTATAAA
34514725 TTTTTAT
1 TTTTTAT
34514732 TAATGGATTA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
18 1 0.01
19 33 0.40
20 17 0.20
21 32 0.39
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTTATAGAATTTTTATAAA
Found at i:34514734 original size:11 final size:10
Alignment explanation
Indices: 34514606--34514731 Score: 80
Period size: 10 Copynumber: 12.7 Consensus size: 10
34514596 TCACTTCAAG
* *
34514606 TTTTTATGAT
1 TTTTTATAAA
34514616 TTTTTAT-AA
1 TTTTTATAAA
**
34514625 TTTTTATACG
1 TTTTTATAAA
* *
34514635 TTTATATCAA
1 TTTTTATAAA
* *
34514645 TTTTAAT-AT
1 TTTTTATAAA
34514654 TTTTTATAAA
1 TTTTTATAAA
34514664 TTTTTATAGAA
1 TTTTTATA-AA
* *
34514675 TTTTAATACA
1 TTTTTATAAA
34514685 TTTTTATAAA
1 TTTTTATAAA
*
34514695 ATTTTA-AATA
1 TTTTTATAA-A
*
34514705 TGTTTTATTAA
1 T-TTTTATAAA
*
34514716 TTTAT-TAAA
1 TTTTTATAAA
34514725 TTTTTAT
1 TTTTTAT
34514732 TAATGGATTA
Statistics
Matches: 87, Mismatches: 22, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
9 24 0.28
10 46 0.53
11 16 0.18
12 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:34514741 original size:19 final size:20
Alignment explanation
Indices: 34514707--34514747 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
34514697 TTTAAATATG
**
34514707 TTTTATTAATTTATTA-AAT
1 TTTTATTAATGGATTAGAAT
34514726 TTTTATTAATGGATTAGAAT
1 TTTTATTAATGGATTAGAAT
34514746 TT
1 TT
34514748 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTTATTAATGGATTAGAAT
Found at i:34514818 original size:10 final size:10
Alignment explanation
Indices: 34514805--34514870 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 10
34514795 TATTTATATC
34514805 TTTTATAATT
1 TTTTATAATT
*
34514815 TTTTACTGATT
1 TTTTA-TAATT
*
34514826 TTTT-TTATT
1 TTTTATAATT
*
34514835 TTTTGTAA-T
1 TTTTATAATT
* *
34514844 TTTCATGATT
1 TTTTATAATT
34514854 TTTTAATAATT
1 TTTT-ATAATT
34514865 TTTTAT
1 TTTTAT
34514871 GAGAAAATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
9 14 0.32
10 13 0.30
11 17 0.39
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:34516534 original size:20 final size:19
Alignment explanation
Indices: 34516509--34516603 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 19
34516499 TGTCCTTATC
*
34516509 TGCACTTCGGTGCCTCTGTT
1 TGCACTTCGGTGCC-CTGTA
34516529 TGCACTTCGGTGCCCTTGTA
1 TGCACTTCGGTGCCC-TGTA
* *
34516549 TGCACTTCAGTGCCCCTGTC
1 TGCACTTCGGTG-CCCTGTA
** *
34516569 TGCACTTCAATACCCTTGTA
1 TGCACTTCGGTGCCC-TGTA
34516589 TGCACTTCGGTGCCC
1 TGCACTTCGGTGCCC
34516604 CTGATGGTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.06
20 56 0.89
21 3 0.05
ACGTcount: A:0.12, C:0.34, G:0.21, T:0.34
Consensus pattern (19 bp):
TGCACTTCGGTGCCCTGTA
Found at i:34516573 original size:40 final size:40
Alignment explanation
Indices: 34516509--34516606 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 40
34516499 TGTCCTTATC
* * ** *
34516509 TGCACTTCGGTGCCTCTGTTTGCACTTCGGTGCCCTTGTA
1 TGCACTTCGGTGCCCCTGTCTGCACTTCAATACCCTTGTA
*
34516549 TGCACTTCAGTGCCCCTGTCTGCACTTCAATACCCTTGTA
1 TGCACTTCGGTGCCCCTGTCTGCACTTCAATACCCTTGTA
34516589 TGCACTTCGGTGCCCCTG
1 TGCACTTCGGTGCCCCTG
34516607 ATGGTATAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.11, C:0.34, G:0.21, T:0.34
Consensus pattern (40 bp):
TGCACTTCGGTGCCCCTGTCTGCACTTCAATACCCTTGTA
Found at i:34523588 original size:26 final size:24
Alignment explanation
Indices: 34523543--34523592 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
34523533 TTATTTACAC
34523543 GATAAACATTAAATTTAATATTAA
1 GATAAACATTAAATTTAATATTAA
*
34523567 GATAATCACTTAAATATTAATATTAA
1 GATAAACA-TTAAAT-TTAATATTAA
34523593 ACTATTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 6 0.26
26 10 0.43
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
GATAAACATTAAATTTAATATTAA
Found at i:34533971 original size:18 final size:18
Alignment explanation
Indices: 34533943--34533986 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
34533933 CACATTTGGT
* *
34533943 GAACCCTCTAAGGTTGTC
1 GAACTCTCTAAGATTGTC
*
34533961 GAGCTCTCTAAGATTGTC
1 GAACTCTCTAAGATTGTC
34533979 GAACTCTC
1 GAACTCTC
34533987 CGTAAGTGGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (18 bp):
GAACTCTCTAAGATTGTC
Found at i:34534212 original size:24 final size:24
Alignment explanation
Indices: 34534191--34534243 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
34534181 GGAAATTTAG
*
34534191 TATTTATTAGCATAATATATTTGA
1 TATTTATTAGCATAAAATATTTGA
* * *
34534215 TGTTTATTAGTATAAAATATTTGT
1 TATTTATTAGCATAAAATATTTGA
34534239 TATTT
1 TATTT
34534244 CTTTCCACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (24 bp):
TATTTATTAGCATAAAATATTTGA
Found at i:34542653 original size:18 final size:19
Alignment explanation
Indices: 34542630--34542672 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
34542620 TAGGAATTAA
*
34542630 TGTTTTAATAAAT-ATTTC
1 TGTTTTAAAAAATAATTTC
34542648 TGTTTTAAAAAATAATTTC
1 TGTTTTAAAAAATAATTTC
*
34542667 TCTTTT
1 TGTTTT
34542673 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (19 bp):
TGTTTTAAAAAATAATTTC
Found at i:34544838 original size:20 final size:18
Alignment explanation
Indices: 34544804--34544857 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
34544794 ATATTAAATT
*
34544804 TAATATTAAGATAATCATAA
1 TAATATTAA-ATAAT-AAAA
34544824 TAATATTAAATTAATAAAA
1 TAATATTAAA-TAATAAAA
*
34544843 TACTATTAAAATAAT
1 TAATATT-AAATAAT
34544858 TATTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (18 bp):
TAATATTAAATAATAAAA
Found at i:34545925 original size:6 final size:6
Alignment explanation
Indices: 34545916--34545995 Score: 94
Period size: 6 Copynumber: 13.3 Consensus size: 6
34545906 TTTTGAATTT
34545916 ATTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
34545964 CTTTAA ATTTAA ATTTAA ATTTAA ATTAAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
34545996 ACTAAAGTCC
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
4 2 0.03
5 6 0.09
6 49 0.75
7 2 0.03
8 6 0.09
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:34545925 original size:17 final size:18
Alignment explanation
Indices: 34545905--34545980 Score: 62
Period size: 17 Copynumber: 4.7 Consensus size: 18
34545895 AGATAAATTG
*
34545905 ATTTTGAATTTAT-TTAA
1 ATTTTAAATTTATCTTAA
34545922 A-TTTAAATTTATCTTAA
1 ATTTTAAATTTATCTTAA
*
34545939 A-TTTAAATTTA-ATT--
1 ATTTTAAATTTATCTTAA
34545953 A-TTTAAATTTA-CTTTAA
1 ATTTTAAATTTATC-TTAA
34545970 A-TTTAAATTTA
1 ATTTTAAATTTA
34545981 AATTTAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 12 0.23
17 27 0.52
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (18 bp):
ATTTTAAATTTATCTTAA
Found at i:34545958 original size:31 final size:29
Alignment explanation
Indices: 34545916--34545990 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 29
34545906 TTTTGAATTT
34545916 ATTTAAATTTAAATTTA-TCTTAAATTTAA
1 ATTTAAATTTAAATTTACT-TTAAATTTAA
34545945 ATTTAATTATTTAAATTTACTTTAAATTTAA
1 ATTTAA--ATTTAAATTTACTTTAAATTTAA
34545976 ATTTAAATTTAAATT
1 ATTTAAATTTAAATT
34545991 AAAATACTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
29 15 0.35
31 27 0.63
32 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTAAATTTAAATTTACTTTAAATTTAA
Found at i:34545961 original size:37 final size:36
Alignment explanation
Indices: 34545914--34545987 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
34545904 GATTTTGAAT
34545914 TTATTTAAATTTAAATTT-ATCTTAAATTTAAATTTAA
1 TTATTTAAATTT-AATTTAAT-TTAAATTTAAATTTAA
*
34545951 TTATTTAAATTTACTTTAAATTTAAATTTAAATTTAA
1 TTATTTAAATTTAATTT-AATTTAAATTTAAATTTAA
34545988 ATTAAAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 4 0.12
37 28 0.82
38 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (36 bp):
TTATTTAAATTTAATTTAATTTAAATTTAAATTTAA
Found at i:34545992 original size:17 final size:18
Alignment explanation
Indices: 34545916--34545995 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 18
34545906 TTTTGAATTT
34545916 ATTTAAATTTAAATTT--
1 ATTTAAATTTAAATTTAA
34545932 ATCTTAAATTTAAATTTAA
1 AT-TTAAATTTAAATTTAA
*
34545951 TTATTTAAATTT-ACTTTAA
1 --ATTTAAATTTAAATTTAA
34545970 ATTTAAATTTAAATTTAA
1 ATTTAAATTTAAATTTAA
*
34545988 ATTAAAAT
1 ATTTAAAT
34545996 ACTAAAGTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.04
17 24 0.44
18 13 0.24
19 6 0.11
20 8 0.15
21 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAAATTTAAATTTAA
Found at i:34546679 original size:16 final size:15
Alignment explanation
Indices: 34546658--34546729 Score: 67
Period size: 16 Copynumber: 4.7 Consensus size: 15
34546648 TAAAAATATT
34546658 ATTAATAATCATAATA
1 ATTAATAAT-ATAATA
34546674 ATTAATAATTATAATA
1 ATTAATAA-TATAATA
* * * *
34546690 AATATTTATGATTATA
1 ATTAATAAT-ATAATA
34546706 ATTAAT-AT-TAATA
1 ATTAATAATATAATA
34546719 ATTAATAATAT
1 ATTAATAATAT
34546730 TAAAAAATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 10 0.22
14 2 0.04
15 4 0.09
16 28 0.62
17 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (15 bp):
ATTAATAATATAATA
Found at i:34546687 original size:13 final size:13
Alignment explanation
Indices: 34546671--34546727 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
34546661 AATAATCATA
34546671 ATAATTAATAATT
1 ATAATTAATAATT
* *
34546684 ATAATAAATATTT
1 ATAATTAATAATT
*
34546697 ATGATT-ATAATT
1 ATAATTAATAATT
34546709 A-ATATTAATAATT
1 ATA-ATTAATAATT
34546722 AATAAT
1 -ATAAT
34546728 ATTAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
12 9 0.26
13 21 0.62
14 3 0.09
15 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
ATAATTAATAATT
Found at i:34546690 original size:19 final size:19
Alignment explanation
Indices: 34546668--34546748 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 19
34546658 ATTAATAATC
34546668 ATAATAATTAATAATTATA
1 ATAATAATTAATAATTATA
* *
34546687 ATAA-ATATTTATGATTATA
1 ATAATA-ATTAATAATTATA
34546706 ATTAAT-ATTAATAA-T-TA
1 A-TAATAATTAATAATTATA
* *
34546723 ATAAT-ATTAAAAAATATA
1 ATAATAATTAATAATTATA
*
34546741 ACAATAAT
1 ATAATAAT
34546749 AAAAGAGGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
16 11 0.22
17 4 0.08
18 8 0.16
19 24 0.48
20 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (19 bp):
ATAATAATTAATAATTATA
Found at i:34546738 original size:13 final size:15
Alignment explanation
Indices: 34546643--34546732 Score: 54
Period size: 16 Copynumber: 5.3 Consensus size: 15
34546633 TTTCAATATC
* *
34546643 ATTAATAAAAATATT
1 ATTAATAATAATAAT
*
34546658 ATTAATAATCATAAT
1 ATTAATAATAATAAT
34546673 AATTAATAATTATAATAAAT
1 -ATTAAT-A--ATAAT-AAT
*
34546693 ATTTATGATTATAATTAAT
1 A-TTA--ATAATAA-TAAT
34546712 ATTAATAATTAATAAT
1 ATTAATAA-TAATAAT
34546728 ATTAA
1 ATTAA
34546733 AAAATATAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
15 12 0.20
16 18 0.31
17 4 0.07
18 3 0.05
19 13 0.22
20 7 0.12
22 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
ATTAATAATAATAAT
Found at i:34547871 original size:30 final size:30
Alignment explanation
Indices: 34547830--34548031 Score: 246
Period size: 30 Copynumber: 6.7 Consensus size: 30
34547820 AATTATCTAG
* *
34547830 AAATTACATTTTGACCCTAAAACTTTTCCT
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
34547860 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
34547890 AAATTACATTTTGACCTCAAGACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
34547920 AAA-TATATATTTAACCCCAAAACTTTTCCA
1 AAATTACAT-TTTGACCCCAAAACTTTTCCA
** * *
34547950 AAATTACATTTCAACCTCAAAAC-TTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTTC-CA
*
34547980 AAATTACATTTTGATCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
34548010 AAATCATATTTTGACCCCAAAA
1 AAATTACATTTTGACCCCAAAA
34548032 TTCCAAAAAT
Statistics
Matches: 146, Mismatches: 22, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
29 8 0.05
30 130 0.89
31 8 0.05
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:34560078 original size:67 final size:68
Alignment explanation
Indices: 34559835--34560438 Score: 975
Period size: 68 Copynumber: 8.9 Consensus size: 68
34559825 ATCATTTCCA
* * * *** *
34559835 ATCCGCTTGAAATTGAAGAAGAGTGGATAACAAGTCTTCACCTCTAAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
34559900 GTC
66 GTC
** *
34559903 ATCCCCTTGAAATTGAAGTAGAGCAGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAT
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
34559968 GTC
66 GTC
34559971 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTC-TTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
34560035 GTC
66 GTC
* *
34560038 AT-CCCTTGAAATTGAAGTAGAGCGGATAACACATCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
34560102 GTC
66 GTC
* * *
34560105 AT-CCCTTGAAATTGAAGTAGAGCGGATAATAAGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
34560169 GTC
66 GTC
* *
34560172 ATCCCCTTAAAATTGAAGTAGAGTGGATAACACGTTTTTTTTCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACG-TCTTTTTCTCTGAAATTGAAGTAAGAGCAA
34560237 CGTC
65 CGTC
*
34560241 ATCCCCTTGAAATTGAAGTAGAGCGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
34560306 GTC
66 GTC
34560309 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGT-TTTTTCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
34560373 GTC
66 GTC
* *
34560376 ATCCTCTTGAAATTG-AGATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCCCTTGAAATTGAAG-TAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCA
34560439 TGATCATTTT
Statistics
Matches: 502, Mismatches: 29, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
66 33 0.07
67 192 0.38
68 212 0.42
69 65 0.13
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (68 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTTTCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:34560599 original size:92 final size:92
Alignment explanation
Indices: 34560442--34560610 Score: 304
Period size: 92 Copynumber: 1.8 Consensus size: 92
34560432 AAGAGCATGA
*
34560442 TCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTATGAAATTG
1 TCATTTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATAACAAGCCTTCGTCCTTATGAAATTG
34560507 AAGTAAGAGTAAGACGAAACATCAACG
66 AAGTAAGAGTAAGACGAAACATCAACG
*
34560534 TCATTTTCCTAT-CTCCTTGAAATTGAAGTAAAACTGGATAACAAGCCTTCGTCCTTCTGAAATT
1 TCATTTTCCTATCCT-CTTGAAATTGAAGTAAAACTGGATAACAAGCCTTCGTCCTTATGAAATT
34560598 GAAGTAAGAGTAA
65 GAAGTAAGAGTAA
34560611 AATGAAGCAT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 2 0.03
92 72 0.97
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (92 bp):
TCATTTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATAACAAGCCTTCGTCCTTATGAAATTG
AAGTAAGAGTAAGACGAAACATCAACG
Found at i:34560909 original size:6 final size:6
Alignment explanation
Indices: 34560900--34560955 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
34560890 TTTTGAATTT
34560900 ATTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTTAA TTATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA --ATTTAA ATTTAA
34560949 A-TTAA AT
1 ATTTAA AT
34560956 ACTAAAGTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 2 0.05
5 7 0.16
6 27 0.61
7 2 0.05
8 6 0.14
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:34560909 original size:17 final size:18
Alignment explanation
Indices: 34560889--34560933 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
34560879 AGATAAATTG
*
34560889 ATTTTGAATTTAT-TTAA
1 ATTTTAAATTTATCTTAA
34560906 A-TTTAAATTTATCTTAA
1 ATTTTAAATTTATCTTAA
34560923 A-TTTAAATTTA
1 ATTTTAAATTTA
34560934 ATTATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTTAAATTTATCTTAA
Found at i:34561638 original size:7 final size:7
Alignment explanation
Indices: 34561626--34561687 Score: 67
Period size: 7 Copynumber: 9.0 Consensus size: 7
34561616 ATAATAATCA
34561626 TAATAAT
1 TAATAAT
34561633 TAATAAT
1 TAATAAT
34561640 TATTATAAT
1 TA--ATAAT
34561649 TAAT-AT
1 TAATAAT
* *
34561655 TTATGAT
1 TAATAAT
34561662 T-ATAAT
1 TAATAAT
34561668 TAAT-AT
1 TAATAAT
34561674 TAATAAT
1 TAATAAT
34561681 TAATAAT
1 TAATAAT
34561688 ATTAAAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
6 16 0.33
7 25 0.52
9 7 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
TAATAAT
Found at i:34561658 original size:13 final size:16
Alignment explanation
Indices: 34561617--34561691 Score: 68
Period size: 16 Copynumber: 4.8 Consensus size: 16
34561607 AAAAATATTA
* *
34561617 TAATAATCATAATAAT
1 TAATAATTATTATAAT
34561633 TAATAATTATTATAAT
1 TAATAATTATTATAAT
*
34561649 TAATATTTATGATTATAAT
1 TAATA---ATTATTATAAT
34561668 TAAT-ATTA--ATAAT
1 TAATAATTATTATAAT
34561681 TAATAA-TATTA
1 TAATAATTATTA
34561692 AAAAATATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
13 11 0.22
14 1 0.02
15 4 0.08
16 19 0.39
19 14 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (16 bp):
TAATAATTATTATAAT
Found at i:34561682 original size:19 final size:19
Alignment explanation
Indices: 34561617--34561687 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
34561607 AAAAATATTA
* *
34561617 TAATAATCATAA-TAATTAA
1 TAATAATTATAATTAA-TAT
*
34561636 TAATTATTATAATTAATAT
1 TAATAATTATAATTAATAT
* *
34561655 TTATGATTATAATTAATAT
1 TAATAATTATAATTAATAT
34561674 TAATAATTAATAAT
1 TAATAATT-ATAAT
34561688 ATTAAAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 35 0.81
20 8 0.19
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
TAATAATTATAATTAATAT
Found at i:34562884 original size:30 final size:30
Alignment explanation
Indices: 34562796--34563000 Score: 220
Period size: 30 Copynumber: 6.9 Consensus size: 30
34562786 CCCTAAATTA
*
34562796 TCCAGAAATTACATTTCGA-CCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
34562826 TCCTAAATTACATTTTGACCCC-AAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
34562855 TCCAAAATTATATTTTGACCCCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* **
34562884 TCTAAAAATTACATTTCAACCCCAAAACTTT
1 TC-CAAAATTACATTTTGACCCCAAAACTTT
** *
34562915 TCCAAAATTACATTTCAACCTCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* * *
34562944 TCTAAAAATTACATTTTTATCCCAAAACTTT
1 TC-CAAAATTACATTTTGACCCCAAAACTTT
* * *
34562975 TTCAAAATCATATTTTGACCCCAAAA
1 TCCAAAATTACATTTTGACCCCAAAA
34563001 TTCCAAAAAA
Statistics
Matches: 148, Mismatches: 21, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
29 48 0.32
30 93 0.63
31 7 0.05
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:34562941 original size:60 final size:60
Alignment explanation
Indices: 34562796--34563058 Score: 270
Period size: 60 Copynumber: 4.4 Consensus size: 60
34562786 CCCTAAATTA
*
34562796 TCCAGAAATTACATTTCGA-CCCAAAACTTTTCCT--AAATTACATTTTGACCCC-AAACTTT
1 TCCA-AAATTACATTTCGACCCCAAAAC-TTT-CTAAAAATTACATTTTTACCCCAAAACTTT
* * **
34562855 TCCAAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTCAACCCCAAAACTTT
1 TCCAAAATTACATTTCGACCCCAAAACTTTCTAAAAATTACATTTTTACCCCAAAACTTT
* * *
34562915 TCCAAAATTACATTTCAACCTCAAAACTTTCTAAAAATTACATTTTTATCCCAAAACTTT
1 TCCAAAATTACATTTCGACCCCAAAACTTTCTAAAAATTACATTTTTACCCCAAAACTTT
* * * * * * * * *
34562975 TTCAAAATCATATTTTGACCCCAAAA-TTCCAAAAAATCACATTTTTGCCCCGAAAC-TT
1 TCCAAAATTACATTTCGACCCCAAAACTTTCTAAAAATTACATTTTTACCCCAAAACTTT
*
34563033 TCAAAAATTACCATTTC-ACCCTCAAA
1 TCCAAAATTA-CATTTCGACCC-CAAA
34563059 CTTCCCTAAA
Statistics
Matches: 170, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
57 2 0.01
58 28 0.16
59 60 0.35
60 80 0.47
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (60 bp):
TCCAAAATTACATTTCGACCCCAAAACTTTCTAAAAATTACATTTTTACCCCAAAACTTT
Found at i:34563048 original size:30 final size:29
Alignment explanation
Indices: 34562801--34563048 Score: 152
Period size: 30 Copynumber: 8.4 Consensus size: 29
34562791 AATTATCCAG
* * **
34562801 AAATTACA-TTTCGACCCAAAACTTTTCCT
1 AAATTACATTTTTGCCCCAAAAC-TTTCAA
*
34562830 AAATTACA-TTTTGACCCC-AAACTTTTCCA
1 AAATTACATTTTTG-CCCCAAAAC-TTTCAA
*
34562859 AAATTATA-TTTTGACCCCAAAACTTTCTAA
1 AAATTACATTTTTG-CCCCAAAACTTTC-AA
*** *
34562889 AAATTACATTTCAACCCCAAAACTTTTCCA
1 AAATTACATTTTTGCCCCAAAAC-TTTCAA
*** *
34562919 AAATTACATTTCAACCTCAAAACTTTCTAA
1 AAATTACATTTTTGCCCCAAAACTTTC-AA
**
34562949 AAATTACATTTTTATCCCAAAACTTTTTC-A
1 AAATTACATTTTTGCCCCAAAAC--TTTCAA
*
34562979 AAA-T-CATATTTTGACCCCAAAA-TTCCAAA
1 AAATTACAT-TTTTG-CCCCAAAACTTTC-AA
* *
34563008 AAATCACATTTTTGCCCCGAAACTTTCAA
1 AAATTACATTTTTGCCCCAAAACTTTCAA
34563037 AAATTACCATTT
1 AAATTA-CATTT
34563049 CACCCTCAAA
Statistics
Matches: 180, Mismatches: 23, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
27 3 0.02
28 3 0.02
29 70 0.39
30 91 0.51
31 9 0.05
32 4 0.02
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (29 bp):
AAATTACATTTTTGCCCCAAAACTTTCAA
Found at i:34564721 original size:31 final size:31
Alignment explanation
Indices: 34564677--34564736 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
34564667 TTTTAGTTAA
* * *
34564677 ATTTGACCCTCAACTTTTTAAAAAGAATCGT
1 ATTTGACCATCAACCTTATAAAAAGAATCGT
*
34564708 ATTTGATCATCAACCTTATAAAAAGAATC
1 ATTTGACCATCAACCTTATAAAAAGAATC
34564737 AAATTATTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (31 bp):
ATTTGACCATCAACCTTATAAAAAGAATCGT
Found at i:34564950 original size:15 final size:17
Alignment explanation
Indices: 34564930--34564963 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34564920 TTTCTATTTA
34564930 TTTGAA-ATTT-TTATT
1 TTTGAATATTTATTATT
34564945 TTTGAATATTTATTATT
1 TTTGAATATTTATTATT
34564962 TT
1 TT
34564964 AAATTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTGAATATTTATTATT
Found at i:34565133 original size:24 final size:25
Alignment explanation
Indices: 34565106--34565159 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
34565096 ATAATTACTC
34565106 TTTAA-AAAAAATTAATAAT-TCAAA
1 TTTAATAAAAAA-TAATAATGTCAAA
*
34565130 TTTAATTAAAAATAATAATGTCAAA
1 TTTAATAAAAAATAATAATGTCAAA
*
34565155 ATTAA
1 TTTAA
34565160 CTACTCATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
TTTAATAAAAAATAATAATGTCAAA
Found at i:34565153 original size:25 final size:25
Alignment explanation
Indices: 34565112--34565159 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
34565102 ACTCTTTAAA
*
34565112 AAAAATTAATAATTCAAATTTAATT
1 AAAAATTAATAATTCAAAATTAATT
34565137 AAAAA-TAATAATGTCAAAATTAA
1 AAAAATTAATAAT-TCAAAATTAA
34565160 CTACTCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAAATTAATAATTCAAAATTAATT
Found at i:34569971 original size:34 final size:33
Alignment explanation
Indices: 34569933--34569998 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 33
34569923 ACTTTAAACC
34569933 ATATATTTCATTAT-TTATTATAT-ATTATTTTTAA
1 ATATATTT--TTATATT-TTATATAATTATTTTTAA
34569967 ATATATTTTTATATTTTATATACATTATTTTT
1 ATATATTTTTATATTTTATATA-ATTATTTTT
34569999 TAACGCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
32 10 0.34
33 2 0.07
34 17 0.59
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (33 bp):
ATATATTTTTATATTTTATATAATTATTTTTAA
Found at i:34570571 original size:23 final size:23
Alignment explanation
Indices: 34570526--34570571 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
34570516 ATTCTTTTTC
* * *
34570526 AAATAAAAAAATTACATAGTGAT
1 AAATAAAAAAACTAAATAATGAT
*
34570549 AAATAAACAAACTAAATAATGAT
1 AAATAAAAAAACTAAATAATGAT
34570572 TTATCTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.24
Consensus pattern (23 bp):
AAATAAAAAAACTAAATAATGAT
Found at i:34575730 original size:18 final size:18
Alignment explanation
Indices: 34575707--34575745 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34575697 AAAAATCAAA
*
34575707 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
34575725 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
34575743 TTT
1 TTT
34575746 GTCTCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:34576784 original size:18 final size:18
Alignment explanation
Indices: 34576759--34576807 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
34576749 TCTTTTTTAT
34576759 TTAT-TTATAAAATATTA
1 TTATATTATAAAATATTA
34576776 TTATATTAT--AATATTA
1 TTATATTATAAAATATTA
*
34576792 TTA-ATAATTAAAATAT
1 TTATATTA-TAAAATAT
34576808 CTTTTGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 4 0.15
18 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATTATAAAATATTA
Found at i:34598005 original size:30 final size:28
Alignment explanation
Indices: 34597958--34598199 Score: 191
Period size: 30 Copynumber: 8.1 Consensus size: 28
34597948 CATAGAAAGT
*
34597958 CCCTGAACTTTCCAAAAATCTCATTTTGA
1 CCCTAAACTTTCCAAAAAT-TCATTTTGA
** *
34597987 CCTCTAAACTTTTTAAAAATT-AGGATTTGA
1 CC-CTAAACTTTCCAAAAATTCA--TTTTGA
*
34598017 CCCCTAAACTTTCCAAAAATTATATTTTGA
1 -CCCTAAACTTTCCAAAAATT-CATTTTGA
* *
34598047 CCCTAAAACTTTCTAAAAAATAT-ATTTTGGT
1 CCCT-AAACTTTC-CAAAAAT-TCATTTT-GA
* *
34598078 CCCTAAACTTTCCAAAAATCACATTTTAA
1 CCCTAAACTTTCCAAAAAT-TCATTTTGA
*
34598107 CCCCTAAACTTTCCAAAAATTACATTTTAA
1 -CCCTAAACTTTCCAAAAATT-CATTTTGA
* *
34598137 CCCTAAAACTTTCTAAAAATTACATTTTAA
1 CCCT-AAACTTTCCAAAAATT-CATTTTGA
* *
34598167 CCTCTAAACTTTGCAAAAATTTGATTTTGA
1 CC-CTAAACTTTCCAAAAA-TTCATTTTGA
34598197 CCC
1 CCC
34598200 CTGAATGTCC
Statistics
Matches: 177, Mismatches: 20, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.01
29 18 0.10
30 139 0.79
31 17 0.10
32 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (28 bp):
CCCTAAACTTTCCAAAAATTCATTTTGA
Found at i:34598034 original size:60 final size:60
Alignment explanation
Indices: 34597958--34598201 Score: 262
Period size: 60 Copynumber: 4.1 Consensus size: 60
34597948 CATAGAAAGT
* * **
34597958 CCCTGAACTTTCCAAAAATCT-CATTTTGACCTCTAAACTTTTTAAAAATTAGGA-TTTGAC
1 CCCTAAACTTTCCAAAAAT-TACATTTTAACCTCTAAACTTTCCAAAAATTA-GATTTTGAC
* * * * * **
34598018 CCCTAAACTTTCCAAAAATTATATTTTGACC-CTAAAACTTTCTAAAAAATATATTTTGGT
1 CCCTAAACTTTCCAAAAATTACATTTTAACCTCT-AAACTTTCCAAAAATTAGATTTTGAC
* * * *
34598078 CCCTAAACTTTCCAAAAATCACATTTTAACCCCTAAACTTTCCAAAAATTACATTTT-AA
1 CCCTAAACTTTCCAAAAATTACATTTTAACCTCTAAACTTTCCAAAAATTAGATTTTGAC
* * *
34598137 CCCTAAAACTTTCTAAAAATTACATTTTAACCTCTAAACTTTGCAAAAATTTGATTTTGAC
1 CCCT-AAACTTTCCAAAAATTACATTTTAACCTCTAAACTTTCCAAAAATTAGATTTTGAC
34598198 CCCT
1 CCCT
34598202 GAATGTCCCA
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
59 8 0.05
60 141 0.90
61 7 0.04
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.36
Consensus pattern (60 bp):
CCCTAAACTTTCCAAAAATTACATTTTAACCTCTAAACTTTCCAAAAATTAGATTTTGAC
Found at i:34598214 original size:90 final size:90
Alignment explanation
Indices: 34597963--34598201 Score: 304
Period size: 90 Copynumber: 2.7 Consensus size: 90
34597953 AAAGTCCCTG
* **
34597963 AACTTTCCAAAAATCT-CATTTTGACCTCTAAACTTTTTAAAAATTAGGA-TTTGACCCCTAAAC
1 AACTTTCTAAAAAT-TACATTTTGACCTCTAAACTTTCCAAAAATTA-GATTTTGACCCCTAAAC
* *
34598026 TTTCCAAAAATTATATTTTGACCCTAA
64 TTTCCAAAAATTACATTTTAACCCTAA
* * * * * *
34598053 AACTTTCTAAAAAATATATTTTGGTCC-CTAAACTTTCCAAAAATCACATTTTAACCCCTAAACT
1 AACTTTCTAAAAATTACATTTT-GACCTCTAAACTTTCCAAAAATTAGATTTTGACCCCTAAACT
34598117 TTCCAAAAATTACATTTTAACCCTAA
65 TTCCAAAAATTACATTTTAACCCTAA
* * *
34598143 AACTTTCTAAAAATTACATTTTAACCTCTAAACTTTGCAAAAATTTGATTTTGACCCCT
1 AACTTTCTAAAAATTACATTTTGACCTCTAAACTTTCCAAAAATTAGATTTTGACCCCT
34598202 GAATGTCCCA
Statistics
Matches: 125, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
89 4 0.03
90 118 0.94
91 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (90 bp):
AACTTTCTAAAAATTACATTTTGACCTCTAAACTTTCCAAAAATTAGATTTTGACCCCTAAACTT
TCCAAAAATTACATTTTAACCCTAA
Found at i:34598668 original size:103 final size:104
Alignment explanation
Indices: 34598548--34598746 Score: 269
Period size: 104 Copynumber: 1.9 Consensus size: 104
34598538 ATATTTTATT
* *
34598548 GAGGCAATGTTTCTTTA-TTTAGGGAACTCGAAAAATTGTGCTCAAACGTACTGGGTACGATTTT
1 GAGGCAATGTTTCTTTATTTTAGGGAACTCGAAAAATTATGCCCAAACGTACTGGGTACGATTTT
*
34598612 T-TTTCGAACCTAAGTAATTGAATATCCTATTAAAAAATC
66 TCTTT-GAACCTAAATAATTGAATATCCTATTAAAAAATC
* ** * ** *
34598651 GAGGCAATG-TTCTTTTATTTTAGGGAAGTCGAGGAATTATGCCCTAACGTGTTGGGTATGATTT
1 GAGGCAATGTTTC-TTTATTTTAGGGAACTCGAAAAATTATGCCCAAACGTACTGGGTACGATTT
34598715 TTCTTTGAACCTAAATAATTGAATATCCTATT
65 TTCTTTGAACCTAAATAATTGAATATCCTATT
34598747 CGGAATCAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
102 3 0.04
103 13 0.16
104 64 0.77
105 3 0.04
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (104 bp):
GAGGCAATGTTTCTTTATTTTAGGGAACTCGAAAAATTATGCCCAAACGTACTGGGTACGATTTT
TCTTTGAACCTAAATAATTGAATATCCTATTAAAAAATC
Found at i:34601497 original size:16 final size:17
Alignment explanation
Indices: 34601473--34601509 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
34601463 CGCATTTGTT
34601473 GCATATGCATT-CATTA
1 GCATATGCATTCCATTA
*
34601489 GCATTTGCATTCCATTA
1 GCATATGCATTCCATTA
34601506 -CATA
1 GCATA
34601510 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (17 bp):
GCATATGCATTCCATTA
Found at i:34603336 original size:19 final size:18
Alignment explanation
Indices: 34603312--34603349 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
34603302 ATTTCACCCA
34603312 AAGAAAAGGAGAAAAAAAG
1 AAGAAAAGGA-AAAAAAAG
34603331 AAGAAAAGGAAAAAAAAG
1 AAGAAAAGGAAAAAAAAG
34603349 A
1 A
34603350 GGAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AAGAAAAGGAAAAAAAAG
Found at i:34604444 original size:49 final size:49
Alignment explanation
Indices: 34604329--34604737 Score: 267
Period size: 50 Copynumber: 8.3 Consensus size: 49
34604319 AAAGATGTGG
* * * * * * *
34604329 AGGGAAAGATTGAAGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCAT-GAAGATATAA
* * *
34604379 TGGG-AAGGATTGAGGCCGCAACGGTGAATCCGATACCATGAAGATACAA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAATCCGATACCATGAAGATATAA
* * * * * *
34604428 AGGGAAAGGTTAAGGCCGCAACGGC-AAACTCGGTACCTTAGAAGACATGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAATC-CGATACCAT-GAAGATATAA
* * *
34604478 TGGG-AAGGATGGAGGCCGCAACGACGAATCCGATACCATGAAGATATGAA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAATCCGATACCATGAAGATAT-AA
* * * *
34604528 A-GGAAAGGTTGAGGCCGCAACGACGAA-CCTGATACCTTAGAAGATGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGCGAATCC-GATACCAT-GAAGATATAA
* * * *
34604577 TGGG-AAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATAA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAATCCGATACCATGAAGATATAA
* * * * * * * * *
34604626 AGGGAAAGGTTAAGGCCGCAATGGCAAAAT-TGGTACCTTAGAAGTTGTGA
1 AGGGAAAGGTTGAGGCCGCAACGGC-GAATCCGATACCAT-GAAGATATAA
* * * * * *
34604676 TGGG-AAGGATTGAGGCTGCAACGGTGAATCCGATACCGTAAAGATATGA
1 AGGGAAAGG-TTGAGGCCGCAACGGCGAATCCGATACCATGAAGATATAA
*
34604725 AGGGAAATGTTGA
1 AGGGAAAGGTTGA
34604738 AACCACAATG
Statistics
Matches: 276, Mismatches: 64, Indels: 39
0.73 0.17 0.10
Matches are distributed among these distances:
48 5 0.02
49 130 0.47
50 137 0.50
51 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.17
Consensus pattern (49 bp):
AGGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCATGAAGATATAA
Found at i:34604462 original size:99 final size:99
Alignment explanation
Indices: 34604329--34604846 Score: 541
Period size: 99 Copynumber: 5.3 Consensus size: 99
34604319 AAAGATGTGG
* * *
34604329 AGGGAAAGATTGAA-GCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAG
1 AGGGAAAGGTT-AAGGCCGCAACGGCAAACTCGGTACCTTAGAAGATGTGATGGGAAGGATTGAG
* *
34604393 GCCGCAACGGTGAATCCGATACCATGAAGATACAA
65 GCCGCAACGGCGAATCCGATACCATGAAGATATAA
** *
34604428 AGGGAAAGGTTAAGGCCGCAACGGCAAACTCGGTACCTTAGAAGACATGATGGGAAGGATGGAGG
1 AGGGAAAGGTTAAGGCCGCAACGGCAAACTCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGG
*
34604493 CCGCAACGACGAATCCGATACCATGAAGATATGAA
66 CCGCAACGGCGAATCCGATACCATGAAGATAT-AA
* * * *
34604528 A-GGAAAGGTTGAGGCCGCAACGACGAAC-CTGATACCTTAGAAGATGTGATGGGAAGGATTGAG
1 AGGGAAAGGTTAAGGCCGCAACGGCAAACTC-GGTACCTTAGAAGATGTGATGGGAAGGATTGAG
* * *
34604591 GTCGCAACGGCGAATCTGGTACCATGAAGATATAA
65 GCCGCAACGGCGAATCCGATACCATGAAGATATAA
* * * *
34604626 AGGGAAAGGTTAAGGCCGCAATGGCAAAATTGGTACCTTAGAAGTTGTGATGGGAAGGATTGAGG
1 AGGGAAAGGTTAAGGCCGCAACGGCAAACTCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGG
* * * * *
34604691 CTGCAACGGTGAATCCGATACCGTAAAGATATGA
66 CCGCAACGGCGAATCCGATACCATGAAGATATAA
* * * * * * * *
34604725 AGGGAAATGTTGAA-ACCACAATGGCAAAC-CTTGTATCTGAG-AGATGTGAT-GGAAAGATTGA
1 AGGGAAAGGTT-AAGGCCGCAACGGCAAACTC-GGTACCTTAGAAGATGTGATGGGAAGGATTGA
* * * * * **
34604786 AGTCGCAACGGCGAATCTTG-TACCATGGAGTTATGG
64 GGCCGCAACGGCGAATC-CGATACCATGAAGATATAA
*
34604822 AGGGAAAGGTTGAA-GCCTCAACGGC
1 AGGGAAAGGTT-AAGGCCGCAACGGC
34604847 GAACCTTATA
Statistics
Matches: 351, Mismatches: 60, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
97 55 0.16
98 15 0.04
99 276 0.79
100 5 0.01
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (99 bp):
AGGGAAAGGTTAAGGCCGCAACGGCAAACTCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGG
CCGCAACGGCGAATCCGATACCATGAAGATATAA
Found at i:34604681 original size:198 final size:197
Alignment explanation
Indices: 34604312--34604846 Score: 644
Period size: 198 Copynumber: 2.7 Consensus size: 197
34604302 GGTAAATCTA
* * * * * *
34604312 ATACCCTAAAGATGTGGAGGGAAAGATTGAAGCCGCAACGGCGAACCCGGTACCTTAGAAGATGT
1 ATACCATAAAGATATGAAAGGAAAGGTTGAAGCCGCAACGGCGAA-CCTGTACCTTAGAAGATGT
* * * * *
34604377 GATGGGAAGGATTGAGGCCGCAACGGTGAATCCGATACCATGAAGATACAAAGGGAAAGGTTAAG
65 GATGGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATAAAGGGAAAGGTTAAG
*
34604442 GCCGCAACGGCAAACTCGGTACCTTAGAAGACATGATGGGAAGGATGGAGGCCGCAACGACGAAT
130 GCCGCAACGGCAAAATCGGTACCTTAGAAGACATGATGGGAAGGATGGAGGCCGCAACGACGAAT
34604507 CCG
195 CCG
* * *
34604510 ATACCATGAAGATATGAAAGGAAAGGTTGAGGCCGCAACGACGAACCTGATACCTTAGAAGATGT
1 ATACCATAAAGATATGAAAGGAAAGGTTGAAGCCGCAACGGCGAACCTG-TACCTTAGAAGATGT
34604575 GATGGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATAAAGGGAAAGGTTAAG
65 GATGGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATAAAGGGAAAGGTTAAG
* * *** * * **
34604640 GCCGCAATGGCAAAATTGGTACCTTAGAAGTTGTGATGGGAAGGATTGAGGCTGCAACGGTGAAT
130 GCCGCAACGGCAAAATCGGTACCTTAGAAGACATGATGGGAAGGATGGAGGCCGCAACGACGAAT
34604705 CCG
195 CCG
* * * * * * * * *
34604708 ATACCGTAAAGATATGAAGGGAAATGTTGAAACCACAATGGCAAACCTTGTATCTGAG-AGATGT
1 ATACCATAAAGATATGAAAGGAAAGGTTGAAGCCGCAACGGCGAACC-TGTACCTTAGAAGATGT
* * * * * **
34604772 GAT-GGAAAGATTGAAGTCGCAACGGCGAATCTTGTACCATGGAGTTATGGAGGGAAAGGTTGAA
65 GATGGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATAAAGGGAAAGGTT-AA
*
34604836 -GCCTCAACGGC
129 GGCCGCAACGGC
34604847 GAACCTTATA
Statistics
Matches: 289, Mismatches: 45, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
196 60 0.21
197 14 0.05
198 213 0.74
199 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.18
Consensus pattern (197 bp):
ATACCATAAAGATATGAAAGGAAAGGTTGAAGCCGCAACGGCGAACCTGTACCTTAGAAGATGTG
ATGGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATAAAGGGAAAGGTTAAGG
CCGCAACGGCAAAATCGGTACCTTAGAAGACATGATGGGAAGGATGGAGGCCGCAACGACGAATC
CG
Found at i:34604835 original size:49 final size:49
Alignment explanation
Indices: 34604775--34604916 Score: 142
Period size: 49 Copynumber: 2.9 Consensus size: 49
34604765 GAGATGTGAT
* * * * *
34604775 GGAAAGATTGAAGTCGCAACGGCGAATCTTGTACCATGGAGTTATGGAG
1 GGAAAGATTGAAGTCACAACGGCGAATCTTATACCATAGAGATATGAAG
* * * * *
34604824 GGAAAGGTTGAAGCCTCAACGGCGAACCTTATACCTTAGAGATATGAAG
1 GGAAAGATTGAAGTCACAACGGCGAATCTTATACCATAGAGATATGAAG
* * * *
34604873 GGAAAGATT-AAGGTCACAATGGCGAATCTCATACCCTAAAGATA
1 GGAAAGATTGAA-GTCACAACGGCGAATCTTATACCATAGAGATA
34604917 GGGAAAAGCA
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
48 2 0.03
49 73 0.97
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (49 bp):
GGAAAGATTGAAGTCACAACGGCGAATCTTATACCATAGAGATATGAAG
Found at i:34604955 original size:21 final size:20
Alignment explanation
Indices: 34604930--34604992 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
34604920 AAAAGCATAT
*
34604930 TGAAGCCGTAAAGGCGAATC
1 TGAAGCTGTAAAGGCGAATC
* *
34604950 TCGAAGTTGTAAAGGGCTAGAT-
1 T-GAAGCTGTAAA-GGCGA-ATC
34604972 TGAAGCTGTAAAGGCGAATC
1 TGAAGCTGTAAAGGCGAATC
34604992 T
1 T
34604993 TACGTCCCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 2 0.06
20 6 0.18
21 19 0.56
22 5 0.15
23 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22
Consensus pattern (20 bp):
TGAAGCTGTAAAGGCGAATC
Found at i:34605171 original size:42 final size:42
Alignment explanation
Indices: 34605124--34605561 Score: 604
Period size: 42 Copynumber: 10.6 Consensus size: 42
34605114 AGAGCAAAGC
*
34605124 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGGTT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* *
34605166 GAAGACATCATCCAATCTATTACCCCGATCATGGGGTAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
34605208 GAAG-C--CATCCAATCCCTTACCCTGATCATGGGACAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
34605247 GAAGACATCATCCAATCTCTTACCCTGATTATAGGGCAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
*
34605289 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGTAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
34605331 AAAG-C--CATCCAATCTCTTACCCCGATCATGAGACAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* *
34605370 GAAGACATCATCCAATCTTTTACCCCGATCATGGGACAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* * *
34605412 GAAGACATCATCTAATCTCTTACCCAGATTATGGGGCAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
** *
34605454 GAAGACATCATCCAATCTCTTACCTTGTTCATGGGGCAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
* *
34605496 GAGGAC--CATCCAATCTCTTACCCCGATCATGGGGTAGATT
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
*
34605536 GAAGACATCATCCAATCTTTTACCCC
1 GAAGACATCATCCAATCTCTTACCCC
34605562 TAAGTCAAGA
Statistics
Matches: 348, Mismatches: 40, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
39 67 0.19
40 37 0.11
41 2 0.01
42 242 0.70
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (42 bp):
GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATT
Found at i:34605343 original size:123 final size:123
Alignment explanation
Indices: 34605124--34605561 Score: 646
Period size: 123 Copynumber: 3.6 Consensus size: 123
34605114 AGAGCAAAGC
* *
34605124 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGGTTGAAGACATCATCCAATCTATTAC
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTAC
*
34605189 CCCGATCATGGGGTAGATTGAAGCCATCCAATCCCTTACCCTGATCATGGGACAGATT
66 CCCGATCATGGGGTAGATTGAAGCCATCCAATCTCTTACCCTGATCATGGGACAGATT
* * *
34605247 GAAGACATCATCCAATCTCTTACCCTGATTATAGGGCAGATTGAAGACATCATCCAATCTCTTAC
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTAC
* * *
34605312 CCCGATCATGGGGTAGATTAAAGCCATCCAATCTCTTACCCCGATCATGAGACAGATT
66 CCCGATCATGGGGTAGATTGAAGCCATCCAATCTCTTACCCTGATCATGGGACAGATT
* * *
34605370 GAAGACATCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAGACATCATCTAATCTCTTAC
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTAC
* * * * * *
34605435 CCAGATTATGGGGCAGATTGAAGACATCATCCAATCTCTTACCTTGTTCATGGGGCAGATT
66 CCCGATCATGGGGTAGATTGAAG-C--CATCCAATCTCTTACCCTGATCATGGGACAGATT
* * *
34605496 GAGGAC--CATCCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTAC
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTAC
34605559 CCC
66 CCC
34605562 TAAGTCAAGA
Statistics
Matches: 281, Mismatches: 31, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
123 192 0.68
124 55 0.20
126 34 0.12
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (123 bp):
GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTAC
CCCGATCATGGGGTAGATTGAAGCCATCCAATCTCTTACCCTGATCATGGGACAGATT
Found at i:34605402 original size:165 final size:166
Alignment explanation
Indices: 34605124--34605561 Score: 677
Period size: 165 Copynumber: 2.7 Consensus size: 166
34605114 AGAGCAAAGC
* *
34605124 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGGTTGAAGACATCATCCAATCTATTAC
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGAC--CATCCAATCTCTTAC
** *
34605189 CCCGATCATGGGGTAGATTGAAG-C--CATCCAATCCCTTACCCTGATCATGGGACAGATTGAAG
64 CCCGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAG
*
34605251 ACATCATCCAATCTCTTACCCTGATTATAGGGCAGATT
129 ACATCATCCAATCTCTTACCCAGATTATAGGGCAGATT
* *
34605289 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGTAGATTAAAG-CCATCCAATCTCTTACCC
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCC
* **
34605353 CGATCATGAGACAGATTGAAGACATCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAGAC
66 CGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAGAC
* *
34605418 ATCATCTAATCTCTTACCCAGATTATGGGGCAGATT
131 ATCATCCAATCTCTTACCCAGATTATAGGGCAGATT
** * *
34605454 GAAGACATCATCCAATCTCTTACCTTGTTCATGGGGCAGATTGAGGACCATCCAATCTCTTACCC
1 GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCC
34605519 CGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCC
66 CGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCC
34605562 TAAGTCAAGA
Statistics
Matches: 247, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
162 34 0.14
163 1 0.00
164 1 0.00
165 153 0.62
166 58 0.23
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (166 bp):
GAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACCATCCAATCTCTTACCC
CGATCATGGGGTAGATTGAAGACATCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAGAC
ATCATCCAATCTCTTACCCAGATTATAGGGCAGATT
Found at i:34607397 original size:30 final size:30
Alignment explanation
Indices: 34607315--34607536 Score: 170
Period size: 30 Copynumber: 7.5 Consensus size: 30
34607305 GAAGTCCTTG
* *
34607315 AACTTTCCAAAAATCACATTTTGA-CTCCA
1 AACTTTCCAAAAATTACATTTTAACCTCCA
* * **
34607344 AACTTTTCAAAAATTA-AGATTTAACCTTTA
1 AACTTTCCAAAAATTACA-TTTTAACCTCCA
* *
34607374 AACTTTGCAAAAATTACATTTTAACC-CTA
1 AACTTTCCAAAAATTACATTTTAACCTCCA
* *** *
34607403 AAATTTCCAAAAA-TACATTTCGGTCCT-TA
1 AACTTTCCAAAAATTACATTT-TAACCTCCA
* * *
34607432 AACTTACCAAAAATCACATTTTAACCCCCA
1 AACTTTCCAAAAATTACATTTTAACCTCCA
* *
34607462 AACTTTCCAAAAATTACATTTTAATCTCGA
1 AACTTTCCAAAAATTACATTTTAACCTCCA
* * *
34607492 ATA-TTTTCAAAAATTACATTTTGACC-CTCG
1 A-ACTTTCCAAAAATTACATTTTAACCTC-CA
34607522 AACTTTCCAAAAATT
1 AACTTTCCAAAAATT
34607537 TTATTTTGAC
Statistics
Matches: 150, Mismatches: 33, Indels: 19
0.74 0.16 0.09
Matches are distributed among these distances:
28 8 0.05
29 50 0.33
30 90 0.60
31 2 0.01
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTAACCTCCA
Found at i:34607414 original size:59 final size:58
Alignment explanation
Indices: 34607315--34607536 Score: 182
Period size: 59 Copynumber: 3.8 Consensus size: 58
34607305 GAAGTCCTTG
* *
34607315 AACTTTCCAAAAATCACATTTTGACTCC-AAACTTTTCAAAAATTAAGATTTAACCTTTA
1 AACTTTCCAAAAATCACATTTTAAC-CCTAAACTTTCCAAAAATTAA-ATTTAACCTTTA
* * * * **
34607374 AACTTTGCAAAAATTACATTTTAACCCTAAAATTTCCAAAAA-TACATTTCGGTCC-TTA
1 AACTTTCCAAAAATCACATTTTAACCCTAAACTTTCCAAAAATTAAATTT--AACCTTTA
* * * * **
34607432 AACTTACCAAAAATCACATTTTAACCCCCAAACTTTCCAAAAATTACATTTTAATCTCGA
1 AACTTTCCAAAAATCACATTTTAA-CCCTAAACTTTCCAAAAATTA-AATTTAACCTTTA
* * * *
34607492 ATA-TTTTCAAAAATTACATTTTGACCCTCGAACTTTCCAAAAATT
1 A-ACTTTCCAAAAATCACATTTTAACCCT-AAACTTTCCAAAAATT
34607537 TTATTTTGAC
Statistics
Matches: 128, Mismatches: 26, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
57 4 0.03
58 28 0.22
59 56 0.44
60 36 0.28
61 4 0.03
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (58 bp):
AACTTTCCAAAAATCACATTTTAACCCTAAACTTTCCAAAAATTAAATTTAACCTTTA
Found at i:34607562 original size:30 final size:30
Alignment explanation
Indices: 34607381--34607563 Score: 104
Period size: 30 Copynumber: 6.2 Consensus size: 30
34607371 TTAAACTTTG
* * * *
34607381 CAAAAATTACATTTTAACCCT-AAAATTTC
1 CAAAAATTACATTTTGACCCTCGAACTTCC
* ** ** *
34607410 CAAAAA-TACATTTCGGTCCTTAAACTTAC
1 CAAAAATTACATTTTGACCCTCGAACTTCC
* * * * *
34607439 CAAAAATCACATTTTAACCCCCAAACTTTC
1 CAAAAATTACATTTTGACCCTCGAACTTCC
** * **
34607469 CAAAAATTACATTTT-AATCTCGAATATTTT
1 CAAAAATTACATTTTGACCCTCGAA-CTTCC
*
34607499 CAAAAATTACATTTTGACCCTCGAACTTTC
1 CAAAAATTACATTTTGACCCTCGAACTTCC
** *
34607529 CAAAAATTTTATTTTGACCCTTGAA-TGTCC
1 CAAAAATTACATTTTGACCCTCGAACT-TCC
34607559 CAAAA
1 CAAAA
34607564 TTTCGAATTT
Statistics
Matches: 120, Mismatches: 29, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
28 10 0.08
29 24 0.20
30 79 0.66
31 7 0.06
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (30 bp):
CAAAAATTACATTTTGACCCTCGAACTTCC
Found at i:34609893 original size:3 final size:3
Alignment explanation
Indices: 34609885--34609912 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34609875 AAATTGACTC
34609885 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
34609913 CTACCATTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:34612897 original size:70 final size:70
Alignment explanation
Indices: 34612816--34613441 Score: 427
Period size: 70 Copynumber: 9.1 Consensus size: 70
34612806 AACAATTAGT
* * * * *
34612816 AGAGTTAAAAGCTCCCAGCTATCGCATTAAGGCTCGTAGGTTCAATACCGCAGCCACCAAACAGT
1 AGAGTTAAAAGCTCCCAGTTGTCGCATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAGT
34612881 TAGCG
66 TAGCG
* * * *
34612886 AGAGTTAAAAGCTCTCAACTT-TTGTC-TTAAGGCTCGTAGGTTCAATACCGCAACCTCCAAACA
1 AGAGTTAAAAGCTC-CCAGTTGTCG-CATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACA
*
34612949 GTTAGCA
64 GTTAGCG
* * *
34612956 AGAGTTAAAAGCTCCCAGTTATCGTC-TTAAGGCTCGCAGGTTCAATATCGCAACCTCCAAACAA
1 AGAGTTAAAAGCTCCCAGTTGTCG-CATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAG
34613020 TT----
65 TTAGCG
* ** * * * *
34613022 --AG---AAAG-ACCCAGTTGTCGTC-TTAAGGCTCATAGGTCCAATACTGCAGCCTCCAAATAG
1 AGAGTTAAAAGCTCCCAGTTGTCG-CATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAG
*
34613080 TTAGTG
65 TTAGCG
* * ** * * * * * *
34613086 AGAGTTAAAAGTTCTCAACTATCGTATTAAGGTTCGCAGGTTTAATACCGTAACCTCAAAACAGT
1 AGAGTTAAAAGCTCCCAGTTGTCGCATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAGT
**
34613151 TAATG
66 TAGCG
** * * * ** * * *
34613156 AGAGTTAAAAGCTCTTAGTTGTCGTATTAAGGTTCGCAAGTTCAATACCATAGCCTCAAAACAAT
1 AGAGTTAAAAGCTCCCAGTTGTCGCATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAGT
*
34613221 TAGTG
66 TAGCG
* ** * ** * * *
34613226 AGGGTTAAAAGCTCCCAACTGTCATC-TTAACACTCGCAGGTTCAATACCGTAGCCCCCAAACAG
1 AGAGTTAAAAGCTCCCAGTTGTC-GCATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAG
* *
34613290 TTTGCT
65 TTAGCG
* ** * * * * * *
34613296 AGAGTTAAAAGCTCCCAATTGTCATATTAAGGTTCGCAGGTTTAATACTGTAACCTCTAAATAGT
1 AGAGTTAAAAGCTCCCAGTTGTCGCATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAGT
*
34613361 TACCG
66 TAGCG
** * * * *** *
34613366 AGAGTTAAAAGCTCTTAGTTGTAGTATTAAGGTTAATAGGTTCAATACCGCAACCTCCAAACAAT
1 AGAGTTAAAAGCTCCCAGTTGTCGCATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAGT
*
34613431 TAGTG
66 TAGCG
34613436 AGAGTT
1 AGAGTT
34613442 CTTAAGGCTT
Statistics
Matches: 439, Mismatches: 101, Indels: 32
0.77 0.18 0.06
Matches are distributed among these distances:
60 44 0.10
61 4 0.01
64 2 0.00
66 2 0.00
69 8 0.02
70 375 0.85
71 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (70 bp):
AGAGTTAAAAGCTCCCAGTTGTCGCATTAAGGCTCGCAGGTTCAATACCGCAACCTCCAAACAGT
TAGCG
Found at i:34613142 original size:130 final size:130
Alignment explanation
Indices: 34612909--34613148 Score: 327
Period size: 130 Copynumber: 1.8 Consensus size: 130
34612899 CTCAACTTTT
* * *
34612909 GTCTTAAGGCTCGTAGGTTCAATACCGCAACCTCCAAACAGTTAGCAAGAGTTAAAAGCTCCCAG
1 GTCTTAAGGCTCATAGGTCCAATACCGCAACCTCCAAACAGTTAGCAAGAGTTAAAAGCTCCCAA
* * * *
34612974 TTATCGTCTTAAGGCTCGCAGGTTCAATATCGCAACCTCCAAACAATTAGAAAGACCCAGTTGTC
66 CTATCGTATTAAGGCTCGCAGGTTCAATACCGCAACCTCAAAACAATTAGAAAGACCCAGTTGTC
* * * ** * *
34613039 GTCTTAAGGCTCATAGGTCCAATACTGCAGCCTCCAAATAGTTAGTGAGAGTTAAAAGTTCTCAA
1 GTCTTAAGGCTCATAGGTCCAATACCGCAACCTCCAAACAGTTAGCAAGAGTTAAAAGCTCCCAA
* * *
34613104 CTATCGTATTAAGGTTCGCAGGTTTAATACCGTAACCTCAAAACA
66 CTATCGTATTAAGGCTCGCAGGTTCAATACCGCAACCTCAAAACA
34613149 GTTAATGAGA
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
130 93 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (130 bp):
GTCTTAAGGCTCATAGGTCCAATACCGCAACCTCCAAACAGTTAGCAAGAGTTAAAAGCTCCCAA
CTATCGTATTAAGGCTCGCAGGTTCAATACCGCAACCTCAAAACAATTAGAAAGACCCAGTTGTC
Found at i:34614004 original size:70 final size:69
Alignment explanation
Indices: 34613915--34614096 Score: 220
Period size: 70 Copynumber: 2.6 Consensus size: 69
34613905 CACACCCTTA
* * * ** *
34613915 CTCGCAGGTTCAATACTGCAACCTCCAAATCGTTAGCGATAGTTAAAAGCTCTCAGTTGTTGTAT
1 CTCGCAAGTTCAATACTGCAACCTCCAAATCGTTAGCGAGAGTTAAAAGCTCCCAACTGTCGTAT
34613980 TAAGG
66 T-AGG
* * * * *
34613985 TTCGCAAGTTCAATACTGCAACCTTCAAATAGTTAGCTAGAGTTAAAAGCTCCCAACTGTCGTCT
1 CTCGCAAGTTCAATACTGCAACCTCCAAATCGTTAGCGAGAGTTAAAAGCTCCCAACTGTCGTAT
34614050 TAGG
66 TAGG
* * *
34614054 CTCGCAAGTTCAACACTGCAGCCTCCAAAACAGTTAGCGAGAG
1 CTCGCAAGTTCAATACTGCAACCTCCAAATC-GTTAGCGAGAG
34614097 CTCAAGCTCC
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
69 28 0.30
70 65 0.70
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (69 bp):
CTCGCAAGTTCAATACTGCAACCTCCAAATCGTTAGCGAGAGTTAAAAGCTCCCAACTGTCGTAT
TAGG
Found at i:34614131 original size:69 final size:69
Alignment explanation
Indices: 34614031--34614187 Score: 174
Period size: 69 Copynumber: 2.3 Consensus size: 69
34614021 CTAGAGTTAA
** * * * *
34614031 AAGCTCCCAACTGTCGTCTTAGGCTCGCAAGTTCAACA-CTGCAGCCTCCAAAACAGTTAGCGA-
1 AAGCTCCCAACTGTAATCTCATGCTCCCAAGTTCAACATC-GCAGCCTCCAAAACAGTAAG-GAC
34614094 GAGCTC
64 GAGCTC
** * * * *
34614100 AAGCTCCCAGTTGTAATCTCATGCTCCCAAGTTTAACATCGCAGCCTTCAAAATAGTAAGTACGA
1 AAGCTCCCAACTGTAATCTCATGCTCCCAAGTTCAACATCGCAGCCTCCAAAACAGTAAGGACGA
34614165 GCTC
66 GCTC
34614169 AAGCTCCCAACTGTAATCT
1 AAGCTCCCAACTGTAATCT
34614188 TAAGGCTCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
68 1 0.01
69 70 0.97
70 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (69 bp):
AAGCTCCCAACTGTAATCTCATGCTCCCAAGTTCAACATCGCAGCCTCCAAAACAGTAAGGACGA
GCTC
Found at i:34614359 original size:69 final size:68
Alignment explanation
Indices: 34614173--34614452 Score: 287
Period size: 69 Copynumber: 4.1 Consensus size: 68
34614163 GAGCTCAAGC
* * * ** *
34614173 TCCCAACTGTAATCTTAAGGCTCATCGGTTTAATATCATGACCTTGAAAACAGCTCGCGGACCTA
1 TCCCAACTGTATTCTAAAGGCTCATCGGTTTAATATCGTGACCTCCAAAACAGCTTGCGGACCTA
34614238 C-T
66 CGT
* * * ** * *
34614240 TCCTAACTGTACTCTTAAGGCTTGTAGGTTTAA-ATCGTGACCTCCAAAACAGCTTGCGGGCCTA
1 TCCCAACTGTATTCTAAAGGCTCATCGGTTTAATATCGTGACCTCCAAAACAGCTTGCGGACCTA
34614304 CGT
66 CGT
* * *
34614307 TCCCAACTGTTATTCTAAAGGCTCACCGGTTTAATATCGCGACCTCCAAAACAACTTGCGGACCT
1 TCCCAACTG-TATTCTAAAGGCTCATCGGTTTAATATCGTGACCTCCAAAACAGCTTGCGGACCT
*
34614372 GCGT
65 ACGT
* * ** * * * *
34614376 TCCTAGCTGATATTCTAAAGGCTTGTCGATTTAATATCGTAACCTCAAAAATAGC-TGACGGACC
1 TCCCAACTG-TATTCTAAAGGCTCATCGGTTTAATATCGTGACCTCCAAAACAGCTTG-CGGACC
34614440 TACGT
64 TACGT
34614445 TCCCAACT
1 TCCCAACT
34614453 CATATTATAG
Statistics
Matches: 173, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
66 27 0.16
67 37 0.21
68 20 0.12
69 89 0.51
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (68 bp):
TCCCAACTGTATTCTAAAGGCTCATCGGTTTAATATCGTGACCTCCAAAACAGCTTGCGGACCTA
CGT
Found at i:34629888 original size:15 final size:15
Alignment explanation
Indices: 34629870--34629905 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
34629860 AATAAAAAAT
34629870 TAAATAAAATAAGGC
1 TAAATAAAATAAGGC
*
34629885 TAAATAAAATAATGC
1 TAAATAAAATAAGGC
34629900 -AAATAA
1 TAAATAA
34629906 TATGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (15 bp):
TAAATAAAATAAGGC
Found at i:34631544 original size:101 final size:99
Alignment explanation
Indices: 34631426--34631894 Score: 358
Period size: 101 Copynumber: 4.6 Consensus size: 99
34631416 ATTTACTGTC
* * * * *
34631426 GTAGCTTCACTCCATTCCACTTCAACTTCAAGAAGATTGAGGTTTGCTATTGTAGTTTTAATCCG
1 GTAGCTTCA-TCTACTCCACTGCAACTTCAAGAAGATTAAGATTTGCT-TTGTAGTTTTAATCCG
* * *
34631491 ATCCACTACAACTTCAAGGATATAGGATTTGATGTA
64 ATCCACTGCAACTTCAGGGATATAGGATTTGATGTT
* * * * * * * * * * *
34631527 GTAGCTTCACTCTATTCCATTGTAGCTTCAGGGAGATTGAGATATGCTTCTGTAATTTTAATTCA
1 GTAGCTTCA-TCTACTCCACTGCAACTTCAAGAAGATTAAGATTTGCTT-TGTAGTTTTAATCCG
* *
34631592 ACCCACTGCAACTTCAGGGGTATAGGATTTGAT-TT
64 ATCCACTGCAACTTCAGGGATATAGGATTTGATGTT
* * * * * *
34631627 GTAGCTTCATCCTGCTCTACTGCAACTTCAA-AGAGA-TAAGAAATCGCTTTCGTAGCTTCAATC
1 GTAGCTTCAT-CTACTCCACTGCAACTTCAAGA-AGATTAAG-ATTTGCTTT-GTAGTTTTAATC
* * * *
34631690 CGATCCGCTGCAACTTTAGGGATATATGATTTGGT-TT
62 CGATCCACTGCAACTTCAGGGATATAGGATTTGATGTT
* * * * * *
34631727 CGTAACTTCATCCTACTCTACTGCAACTTC-AGAGAGA-TAAGGATTCGCGTTCGTAGCTTCAAT
1 -GTAGCTTCAT-CTACTCCACTGCAACTTCAAGA-AGATTAA-GATTTGC-TTTGTAGTTTTAAT
*
34631790 CCGATCCACTGCAACTTCAGGGATATAAGATTTGATGTT
61 CCGATCCACTGCAACTTCAGGGATATAGGATTTGATGTT
* * * *
34631829 GTAGCTTCATTTTGCTCCACTGCAACTTCAAGGAGATAAAGATTTGCTACTATG-AGTTTTAATC
1 GTAGCTTCA-TCTACTCCACTGCAACTTCAAGAAGATTAAGATTTGCT--T-TGTAGTTTTAATC
34631893 CG
62 CG
34631895 CCCCTCTATA
Statistics
Matches: 294, Mismatches: 58, Indels: 31
0.77 0.15 0.08
Matches are distributed among these distances:
99 5 0.02
100 72 0.24
101 195 0.66
102 21 0.07
103 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (99 bp):
GTAGCTTCATCTACTCCACTGCAACTTCAAGAAGATTAAGATTTGCTTTGTAGTTTTAATCCGAT
CCACTGCAACTTCAGGGATATAGGATTTGATGTT
Found at i:34631701 original size:51 final size:50
Alignment explanation
Indices: 34631594--34631872 Score: 201
Period size: 50 Copynumber: 5.5 Consensus size: 50
34631584 TTAATTCAAC
* * * * *
34631594 CCACTGCAACTTCAG-GGGTATAGGATTTGATTT-GTAGCTTC-ATCCTGCT
1 CCACTGCAACTTCAGAGAG-ATAAGATTCGCTTTCGTAGCTTCAATCC-GAT
* * *
34631643 CTACTGCAACTTCAAAGAGATAAGAAATCGCTTTCGTAGCTTCAATCCGAT
1 CCACTGCAACTTCAGAGAGATAAG-ATTCGCTTTCGTAGCTTCAATCCGAT
* * * * * * * * *
34631694 CCGCTGCAACTTTAGGGATATATGATTTGGTTTCGTAACTTC-ATCCTACT
1 CCACTGCAACTTCAGAGAGATAAGATTCGCTTTCGTAGCTTCAATCCGA-T
* *
34631744 CTACTGCAACTTCAGAGAGATAAGGATTCGCGTTCGTAGCTTCAATCCGAT
1 CCACTGCAACTTCAGAGAGATAA-GATTCGCTTTCGTAGCTTCAATCCGAT
* * * * * ** *
34631795 CCACTGCAACTTCAGGGATATAAGATTTGATGTT-GTAGCTTCATTTTGCT
1 CCACTGCAACTTCAGAGAGATAAGATTCGCT-TTCGTAGCTTCAATCCGAT
34631845 CCACTGCAACTTCA-AGGAGATAAAGATT
1 CCACTGCAACTTCAGA-GAGAT-AAGATT
34631873 TGCTACTATG
Statistics
Matches: 177, Mismatches: 43, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
49 22 0.12
50 75 0.42
51 71 0.40
52 9 0.05
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (50 bp):
CCACTGCAACTTCAGAGAGATAAGATTCGCTTTCGTAGCTTCAATCCGAT
Found at i:34631852 original size:50 final size:50
Alignment explanation
Indices: 34631594--34631874 Score: 226
Period size: 51 Copynumber: 5.6 Consensus size: 50
34631584 TTAATTCAAC
* * *
34631594 CCACTGCAACTTCAGGGGTATAGGATTTGATTT-GTAGCTTCATCCTGCT
1 CCACTGCAACTTCAGGGATATAAGATTTGATTTCGTAGCTTCATTCTGCT
* ** * * * * * * *
34631643 CTACTGCAACTTCAAAGAGATAAGAAATCGCTTTCGTAGCTTCAATCCGAT
1 CCACTGCAACTTCAGGGATATAAG-ATTTGATTTCGTAGCTTCATTCTGCT
* * * * * * *
34631694 CCGCTGCAACTTTAGGGATATATGATTTGGTTTCGTAACTTCATCCTACT
1 CCACTGCAACTTCAGGGATATAAGATTTGATTTCGTAGCTTCATTCTGCT
* * * * ** * * *
34631744 CTACTGCAACTTCAGAGAGATAAGGATTCGCGTTCGTAGCTTCAATCCGAT
1 CCACTGCAACTTCAGGGATATAA-GATTTGATTTCGTAGCTTCATTCTGCT
*
34631795 CCACTGCAACTTCAGGGATATAAGATTTGATGTT-GTAGCTTCATTTTGCT
1 CCACTGCAACTTCAGGGATATAAGATTTGAT-TTCGTAGCTTCATTCTGCT
34631845 CCACTGCAACTTCAAGGAGATA-AAGATTTG
1 CCACTGCAACTTC-AGG-GATATAAGATTTG
34631875 CTACTATGAG
Statistics
Matches: 172, Mismatches: 54, Indels: 10
0.73 0.23 0.04
Matches are distributed among these distances:
49 18 0.10
50 70 0.41
51 80 0.47
52 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (50 bp):
CCACTGCAACTTCAGGGATATAAGATTTGATTTCGTAGCTTCATTCTGCT
Found at i:34645231 original size:37 final size:37
Alignment explanation
Indices: 34645162--34645232 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
34645152 TTTCCGGGTA
* * * *
34645162 CAATTGAAGAATACTTATGCAGCGATAGTCTTGGATT
1 CAATTAAAGAATACTTATGCAACGACAATCTTGGATT
*
34645199 CAATTAAAGAATATTTATGCAACGACAATCTTGG
1 CAATTAAAGAATACTTATGCAACGACAATCTTGG
34645233 GTGGATTTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (37 bp):
CAATTAAAGAATACTTATGCAACGACAATCTTGGATT
Found at i:34646462 original size:17 final size:17
Alignment explanation
Indices: 34646391--34646463 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
34646381 CATTGTCCTT
*
34646391 AATGCATTGACAAATGGA
1 AATGCAATGACAAA-GGA
* *
34646409 AATGCAATGATAACA-CA
1 AATGCAATGACAA-AGGA
* ***
34646426 AATGCAGTGACAATTAA
1 AATGCAATGACAAAGGA
34646443 AATGCAATGACAAAGGA
1 AATGCAATGACAAAGGA
34646460 AATG
1 AATG
34646464 TGGTGACAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
17 30 0.71
18 11 0.26
19 1 0.02
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.19
Consensus pattern (17 bp):
AATGCAATGACAAAGGA
Found at i:34646463 original size:34 final size:34
Alignment explanation
Indices: 34646408--34646477 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
34646398 TGACAAATGG
*
34646408 AAATGCAATGATAACACAAATGCAGTGACAATTA
1 AAATGCAATGACAACACAAATGCAGTGACAATTA
* **
34646442 AAATGCAATGACAA-AGGAAATGTGGTGACAATTA
1 AAATGCAATGACAACA-CAAATGCAGTGACAATTA
34646476 AA
1 AA
34646478 TTACAACTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.50, C:0.11, G:0.19, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAACACAAATGCAGTGACAATTA
Found at i:34650906 original size:25 final size:21
Alignment explanation
Indices: 34650889--34650936 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
34650879 AAATATCATA
34650889 AAATAACACATAAATAAATAAT
1 AAATAACA-ATAAATAAATAAT
*
34650911 AAATAATAATAAATAAATAA-
1 AAATAACAATAAATAAATAAT
34650931 AAATAA
1 AAATAA
34650937 ACAAACAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 7 0.28
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (21 bp):
AAATAACAATAAATAAATAAT
Found at i:34650920 original size:10 final size:11
Alignment explanation
Indices: 34650898--34650937 Score: 66
Period size: 10 Copynumber: 3.8 Consensus size: 11
34650888 AAAATAACAC
34650898 ATAAATAAATA
1 ATAAATAAATA
34650909 ATAAAT-AATA
1 ATAAATAAATA
34650919 ATAAATAAATA
1 ATAAATAAATA
34650930 A-AAATAAA
1 ATAAATAAA
34650938 CAAACAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 17 0.61
11 11 0.39
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
ATAAATAAATA
Found at i:34650925 original size:14 final size:14
Alignment explanation
Indices: 34650908--34650951 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
34650898 ATAAATAAAT
34650908 AATAAATAATAATA
1 AATAAATAATAATA
*
34650922 AATAAATAAAAATA
1 AATAAATAATAATA
* * *
34650936 AACAAACAATTATA
1 AATAAATAATAATA
34650950 AA
1 AA
34650952 CAATAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (14 bp):
AATAAATAATAATA
Found at i:34650994 original size:11 final size:11
Alignment explanation
Indices: 34650978--34651025 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
34650968 AGTAGGCATG
*
34650978 AAAATAGATAA
1 AAAATAAATAA
34650989 AAAATAAATAA
1 AAAATAAATAA
*
34651000 AATACAAAAATAA
1 AA-A-ATAAATAA
*
34651013 ATAATAAATAA
1 AAAATAAATAA
34651024 AA
1 AA
34651026 TTAAATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 20 0.67
12 2 0.07
13 8 0.27
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:34651025 original size:17 final size:17
Alignment explanation
Indices: 34650900--34651036 Score: 59
Period size: 17 Copynumber: 7.8 Consensus size: 17
34650890 AATAACACAT
34650900 AAATAAATAATAAATAA
1 AAATAAATAATAAATAA
*
34650917 TAATAAATAAATAAA-AA
1 AAATAAAT-AATAAATAA
* * *
34650934 TAAACAAACAAT-TATAA
1 -AAATAAATAATAAATAA
*
34650951 ACAATAAAATAATAGGAAGTAG
1 A-AAT-AAATAATA--AA-TAA
** * *
34650973 GCATGAA-AATAGATAAA
1 AAATAAATAATAAAT-AA
*
34650990 AAATAAATAA-AATACAA
1 AAATAAATAATAA-ATAA
34651007 AAATAAATAATAAATAA
1 AAATAAATAATAAATAA
*
34651024 AATTAAAT-ATAAA
1 AAATAAATAATAAA
34651037 AGCAAGAATG
Statistics
Matches: 86, Mismatches: 21, Indels: 27
0.64 0.16 0.20
Matches are distributed among these distances:
16 8 0.09
17 45 0.52
18 22 0.26
19 4 0.05
20 2 0.02
21 3 0.03
22 2 0.02
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (17 bp):
AAATAAATAATAAATAA
Found at i:34653797 original size:15 final size:15
Alignment explanation
Indices: 34653777--34653814 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
34653767 ATTTTAATAA
34653777 TTTTATCTT-TTAATT
1 TTTTAT-TTGTTAATT
34653792 TTTTATTTGTTAATT
1 TTTTATTTGTTAATT
34653807 TTTATATT
1 TTT-TATT
34653815 ACATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 15 0.71
16 4 0.19
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTATTTGTTAATT
Found at i:34653860 original size:41 final size:40
Alignment explanation
Indices: 34653801--34653884 Score: 150
Period size: 41 Copynumber: 2.1 Consensus size: 40
34653791 TTTTTATTTG
34653801 TTAATTTTTATATTACATTTATTTTTATTATCATGATAAA
1 TTAATTTTTATATTACATTTATTTTTATTATCATGATAAA
*
34653841 TTAATTTTTTATGTTACATTTATTTTTATTATCATGATAAA
1 TTAA-TTTTTATATTACATTTATTTTTATTATCATGATAAA
34653882 TTA
1 TTA
34653885 GTGTAATTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 4 0.10
41 38 0.90
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (40 bp):
TTAATTTTTATATTACATTTATTTTTATTATCATGATAAA
Found at i:34665820 original size:4 final size:4
Alignment explanation
Indices: 34665813--34665860 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
34665803 AAAAAAAATT
* * *
34665813 CTTC CTTC CTTC CTTC CTT- CTTT CTTC CTTTC TTTC TTTC CTTC CTTC
1 CTTC CTTC CTTC CTTC CTTC CTTC CTTC C-TTC CTTC CTTC CTTC CTTC
34665861 TCTCTACTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.85
5 3 0.08
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (4 bp):
CTTC
Found at i:34666948 original size:17 final size:17
Alignment explanation
Indices: 34666926--34666964 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
34666916 CTCCACCTTG
*
34666926 ACAAGAATTCT-ATACGA
1 ACAAGAACTCTCA-ACGA
34666943 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
34666960 ACAAG
1 ACAAG
34666965 TTCTCCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:34681008 original size:17 final size:17
Alignment explanation
Indices: 34680986--34681035 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
34680976 TTTTGAGATC
34680986 TATTTTAAGTTTAAATT
1 TATTTTAAGTTTAAATT
*
34681003 TATTTTAAATTTAAATT
1 TATTTTAAGTTTAAATT
** *
34681020 TAAATCAAGTTTAAAT
1 TATTTTAAGTTTAAAT
34681036 GAATTTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TATTTTAAGTTTAAATT
Found at i:34682153 original size:12 final size:12
Alignment explanation
Indices: 34682123--34682162 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
34682113 TTTGTTTTTT
34682123 AAATAATAAAAGGG
1 AAATAA-AAAA-GG
*
34682137 GAATAAAAAAGG
1 AAATAAAAAAGG
34682149 AAATAAAAAAGG
1 AAATAAAAAAGG
34682161 AA
1 AA
34682163 TTTTTTTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 15 0.62
13 4 0.17
14 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (12 bp):
AAATAAAAAAGG
Found at i:34682921 original size:60 final size:60
Alignment explanation
Indices: 34682835--34682972 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
34682825 AACTACCCAG
* *
34682835 AAATCACGTTTTAACCCCTTAACTTTCCAAAAGTTATATTTTAACCCCCAAAC-TTTCTAA
1 AAATCACGTTTTAACCCCTCAACTTTCCAAAAATTATATTTTAACCCCCAAACTTTTC-AA
* * **
34682895 AAATCATGTTTTAA-CCCTCAAGCTTTCCAAAAATTATATTTTGACCTTCAAACTTTTCAA
1 AAATCACGTTTTAACCCCTCAA-CTTTCCAAAAATTATATTTTAACCCCCAAACTTTTCAA
* * *
34682955 AAATTACATTTTGACCCC
1 AAATCACGTTTTAACCCC
34682973 CGAACTTCTT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
59 6 0.09
60 52 0.80
61 7 0.11
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
AAATCACGTTTTAACCCCTCAACTTTCCAAAAATTATATTTTAACCCCCAAACTTTTCAA
Found at i:34682979 original size:30 final size:30
Alignment explanation
Indices: 34682855--34683206 Score: 151
Period size: 30 Copynumber: 12.0 Consensus size: 30
34682845 TTAACCCCTT
* * *
34682855 AACTTTCCAAAAGTTATATTTTAACCCCCA
1 AACTTTCCAAAAATTACATTTTAACCCTCA
* * **
34682885 AACTTTCTAAAAATCATGTTTTAACCCTCA
1 AACTTTCCAAAAATTACATTTTAACCCTCA
* * * *
34682915 AGCTTTCCAAAAATTATATTTTGACCTTCA
1 AACTTTCCAAAAATTACATTTTAACCCTCA
* * * *
34682945 AACTTTTCAAAAATTACATTTTGACCCCCG
1 AACTTTCCAAAAATTACATTTTAACCCTCA
** * * *
34682975 AAC-TTCTTTAAAATCACATTTTTACCCTCG
1 AACTTTC-CAAAAATTACATTTTAACCCTCA
* *
34683005 AACTCTCCAAAAATTATCATTTT-A-CCTCG
1 AACTTTCCAAAAATTA-CATTTTAACCCTCA
* * *** *
34683034 AA-TATCTAAAAATTTTGTTTTTGACCCT-A
1 AACTTTCCAAAAA-TTACATTTTAACCCTCA
*
34683063 AACTTTCCAAAAATTACCA-TTT-ACCCCCA
1 AACTTTCCAAAAATTA-CATTTTAACCCTCA
* * *
34683092 AAC--ACCTAAAAATTACCATTTT-ACACTCG
1 AACTTTCC-AAAAATTA-CATTTTAACCCTCA
* * *
34683121 AA-TATCCAAAAATTACATTTTTGACCCT-G
1 AACTTTCCAAAAATTACA-TTTTAACCCTCA
* * * *
34683150 AACTTT-CTAAAACTACCATTTTACCCCT-G
1 AACTTTCCAAAAATTA-CATTTTAACCCTCA
*
34683179 AAC-ATCCAAAAATTACCATTTT-ACCCTC
1 AACTTTCCAAAAATTA-CATTTTAACCCTC
34683207 GAGTGTCCAA
Statistics
Matches: 249, Mismatches: 54, Indels: 39
0.73 0.16 0.11
Matches are distributed among these distances:
27 2 0.01
28 34 0.14
29 80 0.32
30 125 0.50
31 8 0.03
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTAACCCTCA
Found at i:34683014 original size:90 final size:90
Alignment explanation
Indices: 34682855--34683031 Score: 216
Period size: 90 Copynumber: 2.0 Consensus size: 90
34682845 TTAACCCCTT
* * ** *
34682855 AACTTTCCAAAAGTTATATTTTAACCCCCAAACTTTCTAAAAATCATGTTTTAACCCTCAAGCTT
1 AACTTTCCAAAAATTACATTTTAACCCCCAAACTTTCTAAAAATCACATTTTAACCCTCAAGCTC
34682920 TCCAAAAATTAT-ATTTTGACCTTCA
66 TCCAAAAATTATCATTTT-ACCTTCA
* * * * *
34682945 AACTTTTCAAAAATTACATTTTGACCCCCGAAC-TTCTTTAAAATCACATTTTTACCCTCGAA-C
1 AACTTTCCAAAAATTACATTTTAACCCCCAAACTTTC-TAAAAATCACATTTTAACCCTC-AAGC
34683008 TCTCCAAAAATTATCATTTTACCT
64 TCTCCAAAAATTATCATTTTACCT
34683032 CGAATATCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
89 3 0.04
90 64 0.86
91 7 0.09
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (90 bp):
AACTTTCCAAAAATTACATTTTAACCCCCAAACTTTCTAAAAATCACATTTTAACCCTCAAGCTC
TCCAAAAATTATCATTTTACCTTCA
Found at i:34683126 original size:87 final size:86
Alignment explanation
Indices: 34683010--34683228 Score: 264
Period size: 87 Copynumber: 2.5 Consensus size: 86
34683000 CCTCGAACTC
* * ***
34683010 TCCAAAAATTATCATTTTACCTCGAATATCTAAAAATTTTGTTTTTGACCCTAAACTTTCCAAAA
1 TCCAAAAATTACCATTTTACCTCGAATATCCAAAAATTACATTTTTGACCCTAAACTTT-CAAAA
*
34683075 ATTACCA-TTTACCCCCAAACA
65 ACTACCATTTTACCCCCAAACA
* *
34683096 -CCTAAAAATTACCATTTTACACTCGAATATCCAAAAATTACATTTTTGACCCTGAACTTTCTAA
1 TCC-AAAAATTACCATTTTAC-CTCGAATATCCAAAAATTACATTTTTGACCCTAAACTTTCAAA
**
34683160 AACTACCATTTTACCCCTGAACA
64 AACTACCATTTTACCCCCAAACA
* *
34683183 TCCAAAAATTACCATTTTACCCTCGAGTGTCC-AAAATTACCATTTT
1 TCCAAAAATTACCATTTTA-CCTCGAATATCCAAAAATTA-CATTTT
34683229 ACCTCGGGTG
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
85 2 0.02
86 33 0.29
87 77 0.67
88 3 0.03
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.34
Consensus pattern (86 bp):
TCCAAAAATTACCATTTTACCTCGAATATCCAAAAATTACATTTTTGACCCTAAACTTTCAAAAA
CTACCATTTTACCCCCAAACA
Found at i:34683260 original size:27 final size:27
Alignment explanation
Indices: 34683186--34683288 Score: 102
Period size: 28 Copynumber: 3.8 Consensus size: 27
34683176 CTGAACATCC
*
34683186 AAAAATTACCATTTTACCCTCGAGTGT
1 AAAAATTACCATTTTACCCTCGGGTGT
*
34683213 CCAAAATTACCATTTTA-CCTCGGGTGT
1 -AAAAATTACCATTTTACCCTCGGGTGT
* * **
34683240 TAAAATTACCGTTTTACCCTCGGACGTCC
1 AAAAATTACCATTTTACCCTCGG--GTGT
*
34683269 AAAAATTACCGTTTT-CCCTC
1 AAAAATTACCATTTTACCCTC
34683289 AGTATCCAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
26 14 0.22
27 15 0.23
28 20 0.31
29 16 0.25
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (27 bp):
AAAAATTACCATTTTACCCTCGGGTGT
Found at i:34683276 original size:29 final size:29
Alignment explanation
Indices: 34682994--34683304 Score: 164
Period size: 29 Copynumber: 10.9 Consensus size: 29
34682984 AAAATCACAT
* *
34682994 TTTTACCCTCGAACTCTCCAAAAATTATCA
1 TTTTACCCTCGAAC-GTCCAAAAATTACCA
** * ****
34683024 TTTTA-CCTCGAATATCTAAAAATTTTGT
1 TTTTACCCTCGAACGTCCAAAAATTACCA
* *
34683052 TTTTGACCCT-AAACTTTCCAAAAATTACCA
1 TTTT-ACCCTCGAAC-GTCCAAAAATTACCA
* * *
34683082 -TTTACCCCCAAAC-ACCTAAAAATTACCA
1 TTTTACCCTCGAACGTCC-AAAAATTACCA
* **
34683110 TTTTACACTCGAATATCCAAAAATTA-CA
1 TTTTACCCTCGAACGTCCAAAAATTACCA
* * * *
34683138 TTTTTGACCCT-GAACTTTCTAAAACTACCA
1 -TTTT-ACCCTCGAACGTCCAAAAATTACCA
*
34683168 TTTTACCC-CTGAACATCCAAAAATTACCA
1 TTTTACCCTC-GAACGTCCAAAAATTACCA
**
34683197 TTTTACCCTCGAGTGTCC-AAAATTACCA
1 TTTTACCCTCGAACGTCCAAAAATTACCA
* *** *
34683225 TTTTA-CCTCG--GGTGTTAAAATTACCG
1 TTTTACCCTCGAACGTCCAAAAATTACCA
* *
34683251 TTTTACCCTCGGACGTCCAAAAATTACCG
1 TTTTACCCTCGAACGTCCAAAAATTACCA
*
34683280 TTTT-CCCTCAGTA--TCCAAAAATTAC
1 TTTTACCCTC-GAACGTCCAAAAATTAC
34683305 ATTCTTGACT
Statistics
Matches: 220, Mismatches: 43, Indels: 39
0.73 0.14 0.13
Matches are distributed among these distances:
25 2 0.01
26 14 0.06
27 24 0.11
28 55 0.25
29 99 0.45
30 26 0.12
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (29 bp):
TTTTACCCTCGAACGTCCAAAAATTACCA
Done.